count: 30496
list:
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  additionDate: '2016-02-09T13:19:44Z'
  biotoolsCURIE: biotools:mirgen
  biotoolsID: mirgen
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: BastianFromm@gmail.com
    fundrefid: null
    gridid: null
    name: Bastian Fromm
    note: null
    orcidid: https://orcid.org/0000-0003-0352-3037
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    - Support
    url: null
  - email: kevin.j.peterson@dartmouth.edu
    fundrefid: null
    gridid: null
    name: Kevin J. Peterson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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    - Developer
    - Maintainer
    url: null
  - email: support@elixir.no
    fundrefid: null
    gridid: null
    name: The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Support
    url: https://elixir.no/helpdesk
  - email: null
    fundrefid: 10.13039/501100005366
    gridid: grid.5510.1
    name: University of Oslo
    note: null
    orcidid: null
    rorid: 01xtthb56
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uio.no/english/index.html
  description: MirGeneDB is a database of manually curated microRNA genes that have
    been validated and annotated as initially described in Fromm et al. 2015 , Fromm
    et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 )
    includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA
    families from 114 metazoan species. All microRNAs can be browsed, searched and
    downloaded.
  documentation:
  - note: null
    type:
    - General
    url: https://www.mirgenedb.org/information
  download:
  - note: Sequence downloads for 75 species
    type: Biological data
    url: https://www.mirgenedb.org/download
    version: '3.0'
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  - cmd: null
    input:
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        term: Sequence accession (nucleic acid)
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Organism identifier
        uri: http://edamontology.org/data_1869
      format: []
    note: 'Data retrieval: curated miRNA. Organism identifier: a specific miRNA identifier
      or a species  for all miRNAs for that species. Gene transcript report: with
      metadata and visualization. RNA secondary structure: the hairpin loop of the
      miRNA with bases.'
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Gene transcript report
        uri: http://edamontology.org/data_3134
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: RNA secondary structure
        uri: http://edamontology.org/data_0880
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
      - term: BED
        uri: http://edamontology.org/format_3003
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://mirgenedb.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-05T22:33:30.082420Z'
  license: CC0-1.0
  link:
  - note: null
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: MirGeneDB
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: doi
    value: doi:10.25504/FAIRsharing.QXSgvF
    version: '2.0'
  owner: UiO
  publication:
  - doi: 10.1093/nar/gkab1101
    metadata:
      abstract: We describe an update of MirGeneDB, the manually curated microRNA
        gene database. Adhering to uniform and consistent criteria for microRNA annotation
        and nomenclature, we substantially expanded MirGeneDB with 30 additional species
        representing previously missing metazoan phyla such as sponges, jellyfish,
        rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning
        over ∼800 million years of animal evolution, and contains a total number of
        16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this
        update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new
        phylogenetically important species, especially those relevant for the study
        of whole genome duplication events, and through updating evolutionary nodes
        of origin for many families and genes, we were able to substantially refine
        our nomenclature system. All changes are traceable in the specifically developed
        MirGeneDB version tracker. The performance of read-pages is improved and microRNA
        expression matrices for all tissues and species are now also downloadable.
        Altogether, this update represents a significant step toward a complete sampling
        of all major metazoan phyla, and a widely needed foundation for comparative
        microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral
        and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Hoye E.
      - name: Domanska D.
      - name: Zhong X.
      - name: Aparicio-Puerta E.
      - name: Ovchinnikov V.
      - name: Umu S.U.
      - name: Chabot P.J.
      - name: Kang W.
      - name: Aslanzadeh M.
      - name: Tarbier M.
      - name: Marmol-Sanchez E.
      - name: Urgese G.
      - name: Johansen M.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 95
      date: '2022-01-07T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.1: Toward a complete sampling of all major animal phyla'
    note: null
    pmcid: PMC8728216
    pmid: '34850127'
    type:
    - Primary
    version: '2.1'
  - doi: 10.1093/nar/gkz885
    metadata:
      abstract: Small non-coding RNAs have gained substantial attention due to their
        roles in animal development and human disorders. Among them, microRNAs are
        special because individual gene sequences are conserved across the animal
        kingdom. In addition, unique and mechanistically well understood features
        can clearly distinguish bona fide miRNAs from the myriad other small RNAs
        generated by cells. However, making this distinction is not a common practice
        and, thus, not surprisingly, the heterogeneous quality of available miRNA
        complements has become a major concern in microRNA research. We addressed
        this by extensively expanding our curated microRNA gene database-MirGeneDB-to
        45 organisms, encompassing a wide phylogenetic swath of animal evolution.
        By consistently annotating and naming 10,899 microRNA genes in these organisms,
        we show that previous microRNA annotations contained not only many false positives,
        but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA
        complements of closely related organisms are very similar and can be used
        to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust
        platform for microRNA-based research, providing deeper and more significant
        insights into the biology and evolution of miRNAs as well as biomedical and
        biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Domanska D.
      - name: Hoye E.
      - name: Ovchinnikov V.
      - name: Kang W.
      - name: Aparicio-Puerta E.
      - name: Johansen M.
      - name: Flatmark K.
      - name: Mathelier A.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 178
      date: '2020-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.0: The metazoan microRNA complement'
    note: null
    pmcid: PMC6943042
    pmid: '31598695'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1146/annurev-genet-120213-092023
    metadata:
      abstract: Although microRNAs (miRNAs) are among the most intensively studied
        molecules of the past 20 years, determining what is and what is not a miRNA
        has not been straightforward. Here, we present a uniform system for the annotation
        and nomenclature of miRNA genes. We show that less than a third of the 1,881
        human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase
        entries, are robustly supported as miRNA genes. Furthermore, we show that
        the human repertoire of miRNAs has been shaped by periods of intense miRNA
        innovation and that mature gene products show a very different tempo and mode
        of sequence evolution than star products. We establish a new open access database-MirGeneDB
        (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the
        efforts of miRBase but differs from it by annotating the mature versus star
        products and by imposing an evolutionary hierarchy upon this curated and consistently
        named repertoire.
      authors:
      - name: Fromm B.
      - name: Billipp T.
      - name: Peck L.E.
      - name: Johansen M.
      - name: Tarver J.E.
      - name: King B.L.
      - name: Newcomb J.M.
      - name: Sempere L.F.
      - name: Flatmark K.
      - name: Hovig E.
      - name: Peterson K.J.
      citationCount: 435
      date: '2015-11-23T00:00:00Z'
      journal: Annual Review of Genetics
      title: A Uniform System for the Annotation of Vertebrate microRNA Genes and
        the Evolution of the Human microRNAome
    note: null
    pmcid: PMC4743252
    pmid: '26473382'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1093/nar/gkae1094
    metadata:
      abstract: We present a major update of MirGeneDB (3.0), the manually curated
        animal microRNA gene database. Beyond moving to a new server and the creation
        of a computational mirror, we have expanded the database with the addition
        of 33 invertebrate species, including representatives of 5 previously unsampled
        phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA
        genes (5160 of these from the new species) belonging to 1743 microRNA families.
        The inclusion of these new species allowed us to refine both the evolutionary
        node of appearance of a number of microRNA genes/families, as well as MirGeneDB's
        phylogenetically informed nomenclature system. Updated covariance models of
        all microRNA families, along with all smallRNA read data are now downloadable.
        These enhanced annotations will allow researchers to analyze microRNA properties
        such as secondary structure and features of their biogenesis within a robust
        phylogenetic context and without the database plagued with numerous false
        positives and false negatives. In light of these improvements, MirGeneDB 3.0
        will assume the responsibility for naming conserved novel metazoan microRNAs.
        MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely
        available at mirgenedb.org.
      authors:
      - name: Clarke A.W.
      - name: Hoye E.
      - name: Hembrom A.A.
      - name: Paynter V.M.
      - name: Vinther J.
      - name: Wyrozemski L.
      - name: Biryukova I.
      - name: Formaggioni A.
      - name: Ovchinnikov V.
      - name: Herlyn H.
      - name: Pierce A.
      - name: Wu C.
      - name: Aslanzadeh M.
      - name: Cheneby J.
      - name: Martinez P.
      - name: Friedlander M.R.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Umu S.U.
      - name: Johansen M.
      - name: Peterson K.J.
      - name: Fromm B.
      citationCount: 6
      date: '2025-01-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of
        novel conserved microRNA families and updated covariance models'
    note: null
    pmcid: PMC11701709
    pmid: '39673268'
    type:
    - Primary
    version: '3.0'
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  validated: 1
  version:
  - '3.0'
- accessibility: null
  additionDate: '2020-01-14T08:51:18Z'
  biotoolsCURIE: biotools:VADR
  biotoolsID: VADR
  collectionID:
  - COVID-19
  confidence_flag: tool
  cost: null
  credit: []
  description: Classification and annotation of viral sequences based on RefSeq annotation.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    - term: Sequence alignment validation
      uri: http://edamontology.org/operation_0447
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: Reverse complement
      uri: http://edamontology.org/operation_0363
    output: []
  homepage: https://github.com/nawrockie/vadr
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2025-07-05T14:56:17.738501Z'
  license: null
  link: []
  maturity: null
  name: VADR
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/s12859-020-3537-3
    metadata:
      abstract: 'Background: GenBank contains over 3 million viral sequences. The
        National Center for Biotechnology Information (NCBI) previously made available
        a tool for validating and annotating influenza virus sequences that is used
        to check submissions to GenBank. Before this project, there was no analogous
        tool in use for non-influenza viral sequence submissions. Results: We developed
        a system called VADR (Viral Annotation DefineR) that validates and annotates
        viral sequences in GenBank submissions. The annotation system is based on
        the analysis of the input nucleotide sequence using models built from curated
        RefSeqs. Hidden Markov models are used to classify sequences by determining
        the RefSeq they are most similar to, and feature annotation from the RefSeq
        is mapped based on a nucleotide alignment of the full sequence to a covariance
        model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein
        alignments using BLAST. The system identifies 43 types of "alerts" that (unlike
        the previous BLAST-based system) provide deterministic and rigorous feedback
        to researchers who submit sequences with unexpected characteristics. VADR
        has been integrated into GenBank''s submission processing pipeline allowing
        for viral submissions passing all tests to be accepted and annotated automatically,
        without the need for any human (GenBank indexer) intervention. Unlike the
        previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr)
        for local installation and use. VADR has been used for Norovirus submissions
        since May 2018 and for Dengue virus submissions since January 2019. Since
        March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions.
        Other viruses with high numbers of submissions will be added incrementally.
        Conclusion: VADR improves the speed with which non-flu virus submissions to
        GenBank can be checked and improves the content and quality of the GenBank
        annotations. The availability and portability of the software allow researchers
        to run the GenBank checks prior to submitting their viral sequences, and thereby
        gain confidence that their submissions will be accepted immediately without
        the need to correspond with GenBank staff. Reciprocally, the adoption of VADR
        frees GenBank staff to spend more time on services other than checking routine
        viral sequence submissions.'
      authors:
      - name: Schaffer A.A.
      - name: Hatcher E.L.
      - name: Yankie L.
      - name: Shonkwiler L.
      - name: Brister J.R.
      - name: Karsch-Mizrachi I.
      - name: Nawrocki E.P.
      citationCount: 51
      date: '2020-05-24T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'VADR: Validation and annotation of virus sequence submissions to GenBank'
    note: null
    pmcid: PMC7245624
    pmid: '32448124'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Virology
    uri: http://edamontology.org/topic_0781
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-07-04T16:10:32.821423Z'
  biotoolsCURIE: biotools:16smicrobiomemlfs
  biotoolsID: 16smicrobiomemlfs
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: igarachv@ugr.es
    fundrefid: null
    gridid: null
    name: Ignacio Garach Vélez
    note: null
    orcidid: https://orcid.org/0009-0006-6618-7949
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/nach00gar/16SMicrobiomeMLFS
  description: 'Code and supporting data for the article: "Exploring the role of normalization
    and feature selection in microbiome disease classification pipelines."'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function: []
  homepage: https://github.com/nach00gar/16SMicrobiomeMLFS
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-04T16:10:32.823947Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nach00gar/16SMicrobiomeMLFS
  maturity: Emerging
  name: 16SMicrobiomeMLFS
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: igarachv
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:50:32Z'
  biotoolsCURIE: biotools:pyteomics
  biotoolsID: pyteomics
  collectionID:
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: pyteomics@googlegroups.com
    fundrefid: null
    gridid: null
    name: Pyteomics Google Groups
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Issue tracker
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/levitsky/pyteomics/issues
  description: Framework for proteomics data analysis, supporting mzML, MGF, pepXML
    and more.
  documentation:
  - note: null
    type:
    - User manual
    url: https://pyteomics.readthedocs.io/
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/pyteomics/
    version: null
  editPermission:
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    - levitsky
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzXML
        uri: http://edamontology.org/format_3654
    note: null
    operation:
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    output: []
  homepage: https://pyteomics.readthedocs.io/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-04T15:07:26.685242Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/levitsky/pyteomics
  maturity: null
  name: Pyteomics
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1007/s13361-012-0516-6
    metadata:
      abstract: 'Pyteomics is a cross-platform, open-source Python library providing
        a rich set of tools for MS-based proteomics. It provides modules for reading
        LC-MS/MS data, search engine output, protein sequence databases, theoretical
        prediction of retention times, electrochemical properties of polypeptides,
        mass and m/z calculations, and sequence parsing. Pyteomics is available under
        Apache license; release versions are available at the Python Package Index
        http://pypi.python. org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics,
        documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation
        is available at http://packages.python.org/pyteomics.biolccc/. Questions on
        installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com
        [Figure not available: see fulltext.] © 2013 American Society for Mass Spectrometry.'
      authors:
      - name: Goloborodko A.A.
      - name: Levitsky L.I.
      - name: Ivanov M.V.
      - name: Gorshkov M.V.
      citationCount: 141
      date: '2013-02-01T00:00:00Z'
      journal: Journal of the American Society for Mass Spectrometry
      title: Pyteomics - A python framework for exploratory data analysis and rapid
        software prototyping in proteomics
    note: null
    pmcid: null
    pmid: '23292976'
    type:
    - Primary
    version: null
  - doi: 10.1021/acs.jproteome.8b00717
    metadata:
      abstract: Many of the novel ideas that drive today's proteomic technologies
        are focused essentially on experimental or data-processing workflows. The
        latter are implemented and published in a number of ways, from custom scripts
        and programs, to projects built using general-purpose or specialized workflow
        engines; a large part of routine data processing is performed manually or
        with custom scripts that remain unpublished. Facilitating the development
        of reproducible data-processing workflows becomes essential for increasing
        the efficiency of proteomic research. To assist in overcoming the bioinformatics
        challenges in the daily practice of proteomic laboratories, 5 years ago we
        developed and announced Pyteomics, a freely available open-source library
        providing Python interfaces to proteomic data. We summarize the new functionality
        of Pyteomics developed during the time since its introduction.
      authors:
      - name: Levitsky L.I.
      - name: Klein J.A.
      - name: Ivanov M.V.
      - name: Gorshkov M.V.
      citationCount: 117
      date: '2019-02-01T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version:
  - 4.7.5
- accessibility: null
  additionDate: '2023-06-21T16:32:23.746446Z'
  biotoolsCURIE: biotools:massivefold
  biotoolsID: massivefold
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: MassiveFold allows massive sampling with AlphaFold2, AlphaFold3 or
    ColabFold, automatically splitting the computing on CPUs and many GPUs.
  documentation: []
  download: []
  editPermission:
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    type: private
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    input: []
    note: null
    operation:
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    output: []
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  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-03T14:05:33.187978Z'
  license: null
  link: []
  maturity: null
  name: MassiveFold
  operatingSystem:
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  - Mac
  - Windows
  otherID: []
  owner: gbrysbaert
  publication: []
  relation: []
  toolType: []
  topic:
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    uri: http://edamontology.org/topic_0082
  validated: 0
  version:
  - '1.5'
- accessibility: Open access
  additionDate: '2025-07-02T09:38:59.620332Z'
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  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: OmicsQ is a Shiny-based web application designed for preprocessing
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    testing and VSClust for clustering analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/computproteomics/OmicsQ/blob/main/www/tutorial/Tutorial.pdf
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      - term: xlsx
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    note: null
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    output:
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    - data:
        term: Over-representation data
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      format:
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    - data:
        term: Plot
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      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://computproteomics.bmb.sdu.dk/app_direct/OmicsQ/
  homepage_status: 0
  language:
  - R
  - JavaScript
  lastUpdate: '2025-07-02T09:38:59.624571Z'
  license: Apache-2.0
  link:
  - note: null
    type:
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    url: https://github.com/computproteomics/OmicsQ
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  name: OmicsQ
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  owner: veitveit11
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
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  - term: Omics
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  version: []
- accessibility: null
  additionDate: '2017-08-03T18:54:40Z'
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    orcidid: null
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    typeEntity: Person
    typeRole:
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  - note: null
    type:
    - General
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  download: []
  editPermission:
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  function:
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    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3439
    output: []
  homepage: http://cosbi.ku.edu.tr/prism/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-02T08:39:17.732903Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/prism-prediction-of-protein-protein-interactions-and-modeling-their-3d-complexes.html
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  name: PRISM
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  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1093/nar/gku397
    metadata: null
    note: null
    pmcid: PMC4086120
    pmid: '24829450'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2022-02-07T23:41:36.733362Z'
  biotoolsCURIE: biotools:proteinprompt
  biotoolsID: proteinprompt
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: rene.staritzbichler@medizin.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: René Staritzbichler
    note: null
    orcidid: https://orcid.org/0000-0002-6719-2997
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Peter W. Hildebrand
    note: null
    orcidid: https://orcid.org/0000-0003-0063-1104
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Canzler
    note: null
    orcidid: https://orcid.org/0000-0001-7935-9582
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Markus Fischer
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Ulbricht
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nikola Ristic
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A webserver for predicting protein-protein interactions.
  documentation: []
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: null
    operation:
    - term: Protein interaction prediction
      uri: http://edamontology.org/operation_2492
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Protein-protein binding site prediction
      uri: http://edamontology.org/operation_2464
    output: []
  homepage: http://proteinformatics.org/ProteinPrompt
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-02T08:39:17.251278Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.hzdr.de/proteinprompt/ProteinPrompt
  maturity: null
  name: ProteinPrompt
  operatingSystem:
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  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1101/2021.09.03.458859
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
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    uri: http://edamontology.org/topic_0128
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Protein interaction experiment
    uri: http://edamontology.org/topic_3957
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 1
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-07-02T06:56:17.541425Z'
  biotoolsCURIE: biotools:uk_butterfly_monitoring_scheme
  biotoolsID: uk_butterfly_monitoring_scheme
  collectionID:
  - Biodiversity
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: info@butterfly-conservation.org
    fundrefid: null
    gridid: null
    name: Butterfly Conservation
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Contributor
    url: https://butterfly-conservation.org
  - email: null
    fundrefid: null
    gridid: null
    name: UK Centre for Ecology & Hydrology
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://www.ceh.ac.uk
  - email: info@bto.org
    fundrefid: null
    gridid: null
    name: BTO
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Contributor
    url: https://www.bto.org
  - email: null
    fundrefid: null
    gridid: null
    name: JNCC
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Contributor
    url: https://jncc.gov.uk
  description: Long-time series database of of butterfly observations with across
    the UK with rich metadata.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Organism identifier
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      format: []
    - data:
        term: Species name
        uri: http://edamontology.org/data_1045
      format: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Database entry metadata
        uri: http://edamontology.org/data_2193
      format: []
  homepage: https://ukbms.org
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-02T06:56:17.543937Z'
  license: OGTSL
  link:
  - note: Link to data request form.
    type:
    - Service
    url: https://ukbms.org/request-data
  - note: Summary statistics.
    type:
    - Other
    url: https://ukbms.org/official-statistics
  maturity: Mature
  name: UK Butterfly Monitoring Scheme
  operatingSystem: []
  otherID: []
  owner: Keiler_Collier
  publication: []
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  validated: 0
  version: []
- accessibility: null
  additionDate: '2020-01-14T08:51:14Z'
  biotoolsCURIE: biotools:RepeatModeler2
  biotoolsID: RepeatModeler2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: RepeatModeler is a de novo transposable element (TE) family identification
    and modeling package. At the heart of RepeatModeler are three de-novo repeat finding
    programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary
    computational methods for identifying repeat element boundaries and family relationships
    from sequence data.
  documentation: []
  download: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
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  homepage: https://github.com/Dfam-consortium/RepeatModeler
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  language:
  - Perl
  lastUpdate: '2025-07-01T04:28:03.302129Z'
  license: OSL-2.0
  link:
  - note: null
    type:
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    url: https://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSE
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  name: RepeatModeler2
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  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1101/856591
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: repeatmodeler
    type: isNewVersionOf
  toolType:
  - Command-line tool
  topic:
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Mobile genetic elements
    uri: http://edamontology.org/topic_0798
  validated: 1
  version:
  - 2.0.7
- accessibility: Open access
  additionDate: '2025-06-18T09:20:19.874306Z'
  biotoolsCURIE: biotools:chopper
  biotoolsID: chopper
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: decosterwouter@gmail.com
    fundrefid: null
    gridid: null
    name: Wouter de Coster
    note: null
    orcidid: https://orcid.org/0000-0002-5248-8197
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://gigabaseorgigabyte.wordpress.com
  description: Rust implementation of NanoFilt+NanoLyse, both originally written in
    Python. This tool, intended for long read sequencing such as PacBio or ONT, filters
    and trims a fastq file.
  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: 'gunzip -c reads.fastq.gz | chopper -q 10 -l 500 | gzip > filtered_reads.fastq.gz

      chopper -q 10 -l 500 -i reads.fastq > filtered_reads.fastq

      chopper -q 10 -l 500 -i reads.fastq.gz | gzip > filtered_reads.fastq.gz'
    input:
    - data:
        term: Sequence set (nucleic acid)
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      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Box-Whisker plot plotting
      uri: http://edamontology.org/operation_2943
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: JPG
        uri: http://edamontology.org/format_3579
  homepage: https://github.com/wdecoster/chopper
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-30T15:46:01.095401Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/wdecoster/chopper
  maturity: Mature
  name: Chopper
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Keiler_Collier
  publication:
  - doi: 10.1093/bioinformatics/btad311
    metadata:
      abstract: 'Increases in the cohort size in long-read sequencing projects necessitate
        more efficient software for quality assessment and processing of sequencing
        data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe
        novel tools for summarizing experiments, filtering datasets, visualizing phased
        alignments results, and updates to the NanoPack software suite. Availability
        and implementation: The cramino, chopper, kyber, and phasius tools are written
        in Rust and available as executable binaries without requiring installation
        or managing dependencies. Binaries build on musl are available for broad compatibility.
        NanoPlot and NanoComp are written in Python3. Links to the separate tools
        and their documentation can be found at https://github.com/wdecoster/nanopack.
        All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem
        for Linux and are released under the MIT license. The repositories include
        test data, and the tools are continuously tested using GitHub Actions and
        can be installed with the conda dependency manager.'
      authors:
      - name: De Coster W.
      - name: Rademakers R.
      citationCount: 211
      date: '2023-05-01T00:00:00Z'
      journal: Bioinformatics
      title: 'NanoPack2: population-scale evaluation of long-read sequencing data'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: nanopack
    type: isNewVersionOf
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - v0.10.0b
- accessibility: Open access
  additionDate: '2019-11-14T18:08:10Z'
  biotoolsCURIE: biotools:purge_dups
  biotoolsID: purge_dups
  collectionID:
  - ONTeater
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Dengfeng Guan
    note: null
    orcidid: https://orcid.org/0000-0002-6376-3940
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://www.chatlink.com.cn
  description: 'Identifying and removing haplotypic duplication in primary genome
    assemblies | haplotypic duplication identification tool | scripts/pd_config.py:
    script to generate a configuration file used by run_purge_dups.py | purge haplotigs
    and overlaps in an assembly based on read depth | Given a primary assembly pri_asm
    and an alternative assembly hap_asm (optional, if you have one), follow the steps
    shown below to build your own purge_dups pipeline, steps with same number can
    be run simultaneously. Among all the steps, although step 4 is optional, we highly
    recommend our users to do so, because assemblers may produce overrepresented seqeuences.
    In such a case, The final step 4 can be applied to remove those seqeuences'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Read binning
      uri: http://edamontology.org/operation_3798
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/dfguan/purge_dups
  homepage_status: 0
  language:
  - Python
  - C
  lastUpdate: '2025-06-30T15:34:51.626796Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/dfguan/purge_dups
  - note: null
    type:
    - Issue tracker
    url: https://github.com/dfguan/purge_dups/issues
  maturity: null
  name: purge_dups
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1101/729962
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.1.2.6
- accessibility: Open access
  additionDate: '2024-03-18T14:51:49.667412Z'
  biotoolsCURIE: biotools:compleasm
  biotoolsID: compleasm
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: neng@ds.dfci.harvard.edu
    fundrefid: null
    gridid: null
    name: Neng Huang
    note: null
    orcidid: https://orcid.org/0000-0001-7187-0749
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'Compleasm: a faster and more accurate reimplementation of BUSCO.

    It provides measures for quantitative assessment of genome assembly, gene set,
    and transcriptome completeness based on evolutionarily informed expectations of
    gene content from near-universal single-copy orthologs.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/huangnengCSU/compleasm/blob/0.2.6/README.md
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: compleasm run -l "$lineage" -a assembly.fa -o output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    note: Runs compleasm using the BUSCO set corresponding to the lineage given.
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format: []
  homepage: https://github.com/huangnengCSU/compleasm
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-30T15:30:41.266812Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/huangnengCSU/compleasm
  - note: null
    type:
    - Issue tracker
    url: https://github.com/huangnengCSU/compleasm/issues
  - note: List of accepted lineages (taxonomic groups with curated BUSCO sets)
    type:
    - Other
    url: https://busco.ezlab.org/list_of_lineages.html
  maturity: Mature
  name: Compleasm
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication:
  - doi: 10.1093/bioinformatics/btad595
    metadata:
      abstract: 'Motivation: Evaluating the gene completeness is critical to measuring
        the quality of a genome assembly. An incomplete assembly can lead to errors
        in gene predictions, annotation, and other downstream analyses. Benchmarking
        Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing
        the completeness of genome assembly by testing the presence of a set of single-copy
        orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly
        for large genome assemblies. It is cumbersome to apply BUSCO to a large number
        of assemblies. Results: Here, we present compleasm, an efficient tool for
        assessing the completeness of genome assemblies. Compleasm utilizes the miniprot
        protein-to-genome aligner and the conserved orthologous genes from BUSCO.
        It is 14 times faster than BUSCO for human assemblies and reports a more accurate
        completeness of 99.6% than BUSCO''s 95.7%, which is in close agreement with
        the annotation completeness of 99.5% for T2T-CHM13.'
      authors:
      - name: Huang N.
      - name: Li H.
      citationCount: 95
      date: '2023-10-01T00:00:00Z'
      journal: Bioinformatics
      title: 'compleasm: a faster and more accurate reimplementation of BUSCO'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: busco
    type: isNewVersionOf
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - v.0.2.5
- accessibility: null
  additionDate: '2025-06-30T15:03:36.801398Z'
  biotoolsCURIE: biotools:lexicmap
  biotoolsID: lexicmap
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: shenwei356@gmail.com
    fundrefid: null
    gridid: null
    name: Wei Shen
    note: null
    orcidid: https://orcid.org/0000-0002-8099-8258
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://shenwei.me
  description: LexicMap is a nucleotide sequence alignment tool for efficiently querying
    gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions
    of prokaryotic genomes.
  documentation:
  - note: null
    type:
    - User manual
    url: https://bioinf.shenwei.me/LexicMap/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://bioinf.shenwei.me/LexicMap/
  homepage_status: 0
  language:
  - Other
  lastUpdate: '2025-06-30T15:05:12.697639Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/shenwei356/LexicMap
  maturity: null
  name: LexicMap
  operatingSystem: []
  otherID: []
  owner: smeds
  publication:
  - doi: 10.1101/2024.08.30.610459
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version:
  - v0.7.0
  - v0.6.1
  - v0.6.0
  - v0.5.0
  - v0.4.0
  - v0.3.0
  - v0.2.0
  - v0.1.0
- accessibility: Open access
  additionDate: '2016-09-30T15:59:05Z'
  biotoolsCURIE: biotools:silva
  biotoolsID: silva
  collectionID:
  - de.NBI
  - de.NBI-biodata
  - DSMZ Digital Diversity
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: hub@dsmz.de
    fundrefid: null
    gridid: grid.420081.f
    name: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
    note: null
    orcidid: null
    rorid: 02tyer376
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.dsmz.de
  - email: contact@arb-silva.de
    fundrefid: null
    gridid: grid.507782.f
    name: SILVA Team
    note: null
    orcidid: null
    rorid: 027z9pz32
    typeEntity: Division
    typeRole:
    - Primary contact
    url: https://www.arb-silva.de/contact/team/
  description: SILVA provides comprehensive, quality checked and regularly updated
    datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal
    RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://www.arb-silva.de/silva-license-information/
  - note: null
    type:
    - Citation instructions
    url: https://www.arb-silva.de/contact/
  - note: null
    type:
    - General
    url: https://www.arb-silva.de/documentation/
  - note: null
    type:
    - FAQ
    url: https://www.arb-silva.de/documentation/faqs/
  download:
  - note: SILVA dataset archive
    type: Downloads page
    url: https://www.arb-silva.de/download/archive/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Taxon
        uri: http://edamontology.org/data_1868
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Strain name
        uri: http://edamontology.org/data_1046
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Article ID
        uri: http://edamontology.org/data_1088
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Organism name
        uri: http://edamontology.org/data_2909
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: The search and retrieval functions of the SILVA website can be used to build
      custom subsets of sequences. In addition to simple searches e.g. for accession
      numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs,
      complex queries over several database fields using constraints such as sequence
      length or quality values are possible. The results can be sorted according to
      accession numbers, organism names, sequence length, sequence and alignment quality
      and Pintail values. The search results show accession number, organism name,
      sequence length, sequence quality values, taxonomic classifications, and links
      to view the full sequence record on SILVA and on ENA. Sequences found via search
      and added to download cart can be downloaded as FASTA and ARB files.
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    - data:
        term: PCR primers
        uri: http://edamontology.org/data_1240
      format:
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    note: "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences\
      \ of a given probe or primer sequence in the SILVA datasets. \n\nTestPrime allows\
      \ you to evaluate the performance of primer pairs by running an in silico PCR\
      \ on the SILVA databases. From the results of the PCR, TestPrime computes coverages\
      \ for each taxonomic group in all of the taxonomies offered by SILVA."
    operation:
    - term: Primer and probe design
      uri: http://edamontology.org/operation_2419
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    note: The Alignment, Classification and Tree Service (ACT) of SILVA allows to
      align and optionally classify sequences using the SILVA Incremental Aligner
      (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred
      using FastTree or RAxML.
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Phylogenetic inference (maximum likelihood and Bayesian methods)
      uri: http://edamontology.org/operation_0547
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Sequence alignment report
        uri: http://edamontology.org/data_0867
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Taxonomic classification
        uri: http://edamontology.org/data_1872
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.arb-silva.de
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-30T13:26:42.882897Z'
  license: CC-BY-4.0
  link:
  - note: SILVA Taxonomy Browser
    type:
    - Service
    url: https://www.arb-silva.de/browser/
  - note: SILVA metadata search
    type:
    - Service
    url: https://www.arb-silva.de/search/
  - note: 'ACT: Alignment, Classification and Tree Service'
    type:
    - Service
    url: https://www.arb-silva.de/aligner/
  - note: SILVA Probe Match and Evaluation Tool
    type:
    - Service
    url: https://www.arb-silva.de/search/testprobe/
  - note: SILVA Primer Evaluation Tool
    type:
    - Service
    url: https://www.arb-silva.de/search/testprime/
  - note: Web-based viewer for the SILVA guide trees
    type:
    - Service
    url: https://treeviewer.arb-silva.de/
  maturity: Mature
  name: SILVA rRNA database
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_006423
    version: null
  owner: silva
  publication:
  - doi: 10.1093/nar/gks1219
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        web resource for up to date, quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. The referred database release 111 (July
        2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences.
        Since the initial description of the project, substantial new features have
        been introduced, including advanced quality control procedures, an improved
        rRNA gene aligner, online tools for probe and primer evaluation and optimized
        browsing, searching and downloading on the website. Furthermore, the extensively
        curated SILVA taxonomy and the new non-redundant SILVA datasets provide an
        ideal reference for high-throughput classification of data from next-generation
        sequencing approaches. © The Author(s) 2012.
      authors:
      - name: Quast C.
      - name: Pruesse E.
      - name: Yilmaz P.
      - name: Gerken J.
      - name: Schweer T.
      - name: Yarza P.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 22633
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The SILVA ribosomal RNA gene database project: Improved data processing
        and web-based tools'
    note: null
    pmcid: PMC3531112
    pmid: '23193283'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkt1209
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        resource for up-to-date quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. SILVA provides a manually curated taxonomy
        for all three domains of life, based on representative phylogenetic trees
        for the small- and large-subunit rRNA genes. This article describes the improvements
        the SILVA taxonomy has undergone in the last 3 years. Specifically we are
        focusing on the curation process, the various resources used for curation
        and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies.
        Our comparisons not only revealed a reasonable overlap between the taxa names,
        but also points to significant differences in both names and numbers of taxa
        between the three resources. © 2013 The Author(s). Published by Oxford University
        Press.
      authors:
      - name: Yilmaz P.
      - name: Parfrey L.W.
      - name: Yarza P.
      - name: Gerken J.
      - name: Pruesse E.
      - name: Quast C.
      - name: Schweer T.
      - name: Peplies J.
      - name: Ludwig W.
      - name: Glockner F.O.
      citationCount: 2590
      date: '2014-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: The SILVA and "all-species Living Tree Project (LTP)" taxonomic frameworks
    note: null
    pmcid: PMC3965112
    pmid: '24293649'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkm864
    metadata:
      abstract: 'Sequencing ribosomal RNA (rRNA) genes is currently the method of
        choice for phylogenetic reconstruction, nucleic acid based detection and quantification
        of microbial diversity. The ARB software suite with its corresponding rRNA
        datasets has been accepted by researchers worldwide as a standard tool for
        large scale rRNA analysis. However, the rapid increase of publicly available
        rRNA sequence data has recently hampered the maintenance of comprehensive
        and curated rRNA knowledge databases. A new system, SILVA (from Latin silva,
        forest), was implemented to provide a central comprehensive web resource for
        up to date, quality controlled databases of aligned rRNA sequences from the
        Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies,
        carry a rich set of sequence associated contextual information, have multiple
        taxonomic classifications, and the latest validly described nomenclature.
        Furthermore, two precompiled sequence datasets compatible with ARB are offered
        for download on the SILVA website: (i) the reference (Ref) datasets, comprising
        only high quality, nearly full length sequences suitable for in-depth phylogenetic
        analysis and probe design and (ii) the comprehensive Parc datasets with all
        publicly available rRNA sequences longer than 300 nucleotides suitable for
        biodiversity analyses. The latest publicly available database release 91 (August
        2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689
        large subunit rRNAs. © 2007 The Author(s).'
      authors:
      - name: Pruesse E.
      - name: Quast C.
      - name: Knittel K.
      - name: Fuchs B.M.
      - name: Ludwig W.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 5291
      date: '2007-12-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'SILVA: A comprehensive online resource for quality checked and aligned
        ribosomal RNA sequence data compatible with ARB'
    note: null
    pmcid: PMC2175337
    pmid: '17947321'
    type:
    - Other
    version: null
  - doi: 10.1093/bioinformatics/bts252
    metadata:
      abstract: 'Motivation: In the analysis of homologous sequences, computation
        of multiple sequence alignments (MSAs) has become a bottleneck. This is especially
        troublesome for marker genes like the ribosomal RNA (rRNA) where already millions
        of sequences are publicly available and individual studies can easily produce
        hundreds of thousands of new sequences. Methods have been developed to cope
        with such numbers, but further improvements are needed to meet accuracy requirements.Results:
        In this study, we present the SILVA Incremental Aligner (SINA) used to align
        the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA
        uses a combination of k-mer searching and partial order alignment (POA) to
        maintain very high alignment accuracy while satisfying high throughput performance
        demands. SINA was evaluated in comparison with the commonly used high throughput
        MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could
        be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising
        38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference
        MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy
        than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012.
        Published by Oxford University Press.'
      authors:
      - name: Pruesse E.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 2408
      date: '2012-07-01T00:00:00Z'
      journal: Bioinformatics
      title: 'SINA: Accurate high-throughput multiple sequence alignment of ribosomal
        RNA genes'
    note: null
    pmcid: PMC3389763
    pmid: '22556368'
    type:
    - Other
    version: null
  - doi: 10.1016/j.jbiotec.2017.06.1198
    metadata:
      abstract: SILVA (lat. forest) is a comprehensive web resource, providing services
        around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA)
        sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back
        to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich
        started the integrated software workbench ARB (lat. tree) to support high-quality
        phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes.
        At that time, the ARB project maintained both, the sequence reference datasets
        and the software package for data analysis. In 2005, with the massive increase
        of DNA sequence data, the maintenance of the software system ARB and the corresponding
        rRNA databases SILVA was split between Munich and the Microbial Genomics and
        Bioinformatics Research Group in Bremen. ARB has been continuously developed
        to include new features and improve the usability of the workbench. Thousands
        of users worldwide appreciate the seamless integration of common analysis
        tools under a central graphical user interface, in combination with its versatility.
        The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA
        release 89. Since then, full SILVA releases offering the database content
        in various flavours are published at least annually, complemented by intermediate
        web-releases where only the SILVA web dataset is updated. SILVA is the only
        rDNA database project worldwide where special emphasis is given to the consistent
        naming of clades of uncultivated (environmental) sequences, where no validly
        described cultivated representatives are available. Also exclusive for SILVA
        is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S
        rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed
        to include Eukaryota, another unique feature among rDNA databases. With the
        termination of the European Ribosomal RNA Database Project in 2007, the SILVA
        database has become the authoritative rDNA database project for Europe. The
        application spectrum of ARB and SILVA ranges from biodiversity analysis, medical
        diagnostics, to biotechnology and quality control for academia and industry.
      authors:
      - name: Glockner F.O.
      - name: Yilmaz P.
      - name: Quast C.
      - name: Gerken J.
      - name: Beccati A.
      - name: Ciuprina A.
      - name: Bruns G.
      - name: Yarza P.
      - name: Peplies J.
      - name: Westram R.
      - name: Ludwig W.
      citationCount: 635
      date: '2017-11-10T00:00:00Z'
      journal: Journal of Biotechnology
      title: 25 years of serving the community with ribosomal RNA gene reference databases
        and tools
    note: null
    pmcid: null
    pmid: '28648396'
    type:
    - Review
    version: null
  - doi: 10.1186/s12859-017-1841-3
    metadata:
      abstract: 'Background: Phylogenetic trees are an important tool to study the
        evolutionary relationships among organisms. The huge amount of available taxa
        poses difficulties in their interactive visualization. This hampers the interaction
        with the users to provide feedback for the further improvement of the taxonomic
        framework. Results: The SILVA Tree Viewer is a web application designed for
        visualizing large phylogenetic trees without requiring the download of any
        software tool or data files. The SILVA Tree Viewer is based on Web Geographic
        Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables
        zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer
        enables access to two phylogenetic (guide) trees provided by the SILVA database:
        the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences,
        clustered at 99% sequence identity and the LSU Ref inferred from high-quality,
        full-length large subunit sequences. Conclusions: The Tree Viewer provides
        tree navigation, search and browse tools as well as an interactive feedback
        system to collect any kinds of requests ranging from taxonomy to data curation
        and improving the tool itself.'
      authors:
      - name: Beccati A.
      - name: Gerken J.
      - name: Quast C.
      - name: Yilmaz P.
      - name: Glockner F.O.
      citationCount: 29
      date: '2017-09-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'SILVA tree viewer: Interactive web browsing of the SILVA phylogenetic
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    note: null
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  - term: Sequence analysis
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  - term: Phylogenetics
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  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Probes and primers
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  validated: 1
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  description: SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon
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  publication:
  - doi: 10.1093/nar/gks1219
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        web resource for up to date, quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. The referred database release 111 (July
        2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences.
        Since the initial description of the project, substantial new features have
        been introduced, including advanced quality control procedures, an improved
        rRNA gene aligner, online tools for probe and primer evaluation and optimized
        browsing, searching and downloading on the website. Furthermore, the extensively
        curated SILVA taxonomy and the new non-redundant SILVA datasets provide an
        ideal reference for high-throughput classification of data from next-generation
        sequencing approaches. © The Author(s) 2012.
      authors:
      - name: Quast C.
      - name: Pruesse E.
      - name: Yilmaz P.
      - name: Gerken J.
      - name: Schweer T.
      - name: Yarza P.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 22633
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The SILVA ribosomal RNA gene database project: Improved data processing
        and web-based tools'
    note: null
    pmcid: PMC3531112
    pmid: '23193283'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkt1209
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        resource for up-to-date quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. SILVA provides a manually curated taxonomy
        for all three domains of life, based on representative phylogenetic trees
        for the small- and large-subunit rRNA genes. This article describes the improvements
        the SILVA taxonomy has undergone in the last 3 years. Specifically we are
        focusing on the curation process, the various resources used for curation
        and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies.
        Our comparisons not only revealed a reasonable overlap between the taxa names,
        but also points to significant differences in both names and numbers of taxa
        between the three resources. © 2013 The Author(s). Published by Oxford University
        Press.
      authors:
      - name: Yilmaz P.
      - name: Parfrey L.W.
      - name: Yarza P.
      - name: Gerken J.
      - name: Pruesse E.
      - name: Quast C.
      - name: Schweer T.
      - name: Peplies J.
      - name: Ludwig W.
      - name: Glockner F.O.
      citationCount: 2590
      date: '2014-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: The SILVA and "all-species Living Tree Project (LTP)" taxonomic frameworks
    note: null
    pmcid: PMC3965112
    pmid: '24293649'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/bts252
    metadata:
      abstract: 'Motivation: In the analysis of homologous sequences, computation
        of multiple sequence alignments (MSAs) has become a bottleneck. This is especially
        troublesome for marker genes like the ribosomal RNA (rRNA) where already millions
        of sequences are publicly available and individual studies can easily produce
        hundreds of thousands of new sequences. Methods have been developed to cope
        with such numbers, but further improvements are needed to meet accuracy requirements.Results:
        In this study, we present the SILVA Incremental Aligner (SINA) used to align
        the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA
        uses a combination of k-mer searching and partial order alignment (POA) to
        maintain very high alignment accuracy while satisfying high throughput performance
        demands. SINA was evaluated in comparison with the commonly used high throughput
        MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could
        be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising
        38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference
        MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy
        than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012.
        Published by Oxford University Press.'
      authors:
      - name: Pruesse E.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 2408
      date: '2012-07-01T00:00:00Z'
      journal: Bioinformatics
      title: 'SINA: Accurate high-throughput multiple sequence alignment of ribosomal
        RNA genes'
    note: null
    pmcid: PMC3389763
    pmid: '22556368'
    type:
    - Primary
    version: null
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  - term: Taxonomy
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  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
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  description: 'FAIR EVA: Evaluator, Validator & Advisor has been developed to check
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      authors:
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      - name: Bernal I.
      citationCount: 6
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  additionDate: '2025-06-30T07:14:20.248231Z'
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- accessibility: null
  additionDate: '2025-06-27T08:20:38.689434Z'
  biotoolsCURIE: biotools:kite
  biotoolsID: kite
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A Java application aiming to detect any combination of microbe genomes
    selected to be detected from metagenome data
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/HEAP-EXPOSOME/KITE
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-27T08:20:46.074120Z'
  license: null
  link: []
  maturity: null
  name: KITE
  operatingSystem: []
  otherID: []
  owner: roxana.martinez
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-06-26T12:43:43.738614Z'
  biotoolsCURIE: biotools:dalia
  biotoolsID: dalia
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sonja Herres-Pawlis
    note: null
    orcidid: https://orcid.org/0000-0002-4354-4353
    rorid: 04xfq0f34
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: DALIA promotes the learning and teaching of Data Literacy through the
    curated supply of open teaching and learning content, empowering everyone to collect,
    analyze, critically evaluate, and use data in a FAIR way.
  documentation: []
  download: []
  editPermission:
    authors:
    - jortmeyer
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://search.dalia.education
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-26T13:20:18.702036Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://git.rwth-aachen.de/dalia
  - note: null
    type:
    - Social media
    url: https://nfdi.social/@dalia
  - note: null
    type:
    - Social media
    url: https://bsky.app/profile/daliaeducation.bsky.social
  - note: Newsletter
    type:
    - Other
    url: https://dalia.education/en/newsletter
  maturity: Emerging
  name: DALIA
  operatingSystem:
  - Linux
  otherID: []
  owner: cthoyt
  publication: []
  relation: []
  toolType:
  - Web application
  - Database portal
  - SPARQL endpoint
  - Web API
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-08-26T14:34:55Z'
  biotoolsCURIE: biotools:MINERVA_Platform
  biotoolsID: MINERVA_Platform
  collectionID:
  - ELIXIR-LU
  - LCSB
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform
    is a standalone webserver for visualization, exploration and management of molecular
    networks encoded in SBGN-compliant format, including files produced using CellDesigner
    or SBGN editors. Visualization of uploaded networks generated by the platform
    is accessible via a web browser to all viewers with the weblink to the resource.


    The MINERVA Platform is a webservice using the Java Server Faces 2 technology.
    The server side, including data parsing, integration, annotation and verification,
    is implemented in Java. The platform uses the Postgres SQL database for data storage
    and the Hibernate framework as a middle layer between web server and database.
    The user web-interface is generated using React.js. The displayed content is visualized
    by OpenLayers API, dedicated JavaScript and CSS.'
  documentation:
  - note: null
    type:
    - Quick start guide
    - Release notes
    - User manual
    - API documentation
    - Citation instructions
    - Terms of use
    url: https://minerva.uni.lu
  download:
  - note: Installation instructions, including debian package, virtual machine images
      and docker containers.
    type: Other
    url: https://minerva.pages.uni.lu/doc/install/
    version: 13.1.3 - 18.1.1
  editPermission:
    authors:
    - sascha.herzinger
    type: group
  elixirCommunity: []
  elixirNode:
  - Luxembourg
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Visualise systems biology diagrams online, on a standalone web server
    operation:
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    output: []
  - cmd: null
    input: []
    note: Visualise omics data from multiple datasets on top of the diagrams
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output: []
  - cmd: null
    input: []
    note: 'Convert between main systems biology layout formats: CellDeslgners SBML,
      SBML layout+render, SBGN-ML, GPML'
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  - cmd: null
    input: []
    note: Use MINERVA API to access systems biology formats for modelling
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://minerva.uni.lu
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-26T13:15:59.673112Z'
  license: AGPL-3.0
  link:
  - note: GiLab repository for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/core/
  - note: Issue tracker for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Issue tracker
    url: https://gitlab.lcsb.uni.lu/minerva/core/-/issues
  - note: GiLab repository for frontend functionalities
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/frontend
  - note: Issue tracker for frontend functionalities
    type:
    - Issue tracker
    url: https://gitlab.lcsb.uni.lu/minerva/frontend/-/issues
  maturity: Mature
  name: The MINERVA Platform
  operatingSystem: []
  otherID: []
  owner: mjostaszewski
  publication:
  - doi: 10.1038/npjsba.2016.20
    metadata:
      abstract: Our growing knowledge about various molecular mechanisms is becoming
        increasingly more structured and accessible. Different repositories of molecular
        interactions and available literature enable construction of focused and high-quality
        molecular interaction networks. Novel tools for curation and exploration of
        such networks are needed, in order to foster the development of a systems
        biology environment. In particular, solutions for visualization, annotation
        and data cross-linking will facilitate usage of network-encoded knowledge
        in biomedical research. To this end we developed the MINERVA (Molecular Interaction
        NEtwoRks VisuAlization) platform, a standalone webservice supporting curation,
        annotation and visualization of molecular interaction networks in Systems
        Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated
        content annotation and verification for improved quality control. The end
        users can explore and interact with hosted networks, and provide direct feedback
        to content curators. MINERVA enables mapping drug targets or overlaying experimental
        data on the visualized networks. Extensive export functions enable downloading
        areas of the visualized networks as SBGN-compliant models for efficient reuse
        of hosted networks. The software is available under Affero GPL 3.0 as a Virtual
        Machine snapshot, Debian package and Docker instance at http://r3lab.uni.lu/web/minerva-website/.
        We believe that MINERVA is an important contribution to systems biology community,
        as its architecture enables set-up of locally or globally accessible SBGN-oriented
        repositories of molecular interaction networks. Its functionalities allow
        overlay of multiple information layers, facilitating exploration of content
        and interpretation of data. Moreover, annotation and verification workflows
        of MINERVA improve the efficiency of curation of networks, allowing life-science
        researchers to better engage in development and use of biomedical knowledge
        repositories.
      authors:
      - name: Gawron P.
      - name: Ostaszewski M.
      - name: Satagopam V.
      - name: Gebel S.
      - name: Mazein A.
      - name: Kuzma M.
      - name: Zorzan S.
      - name: McGee F.
      - name: Otjacques B.
      - name: Balling R.
      - name: Schneider R.
      citationCount: 65
      date: '2016-01-01T00:00:00Z'
      journal: npj Systems Biology and Applications
      title: MINERVA—A platform for visualization and curation of molecular interaction
        networks
    note: null
    pmcid: PMC5516855
    pmid: '28725475'
    type:
    - Primary
    version: '10.0'
  - doi: 10.1093/bioinformatics/btz286
    metadata:
      abstract: 'Summary: The complexity of molecular networks makes them difficult
        to navigate and interpret, creating a need for specialized software. MINERVA
        is a web platform for visualization, exploration and management of molecular
        networks. Here, we introduce an extension to MINERVA architecture that greatly
        facilitates the access and use of the stored molecular network data. It allows
        to incorporate such data in analytical pipelines via a programmatic access
        interface, and to extend the platform''s visual exploration and analytics
        functionality via plugin architecture. This is possible for any molecular
        network hosted by the MINERVA platform encoded in well-recognized systems
        biology formats. To showcase the possibilities of the plugin architecture,
        we have developed several plugins extending the MINERVA core functionalities.
        In the article, we demonstrate the plugins for interactive tree traversal
        of molecular networks, for enrichment analysis and for mapping and visualization
        of known disease variants or known adverse drug reactions to molecules in
        the network. Availability and implementation: Plugins developed and maintained
        by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/.
        The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.'
      authors:
      - name: Hoksza D.
      - name: Gawron P.
      - name: Ostaszewski M.
      - name: Smula E.
      - name: Schneider R.
      citationCount: 25
      date: '2019-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'MINERVA API and plugins: Opening molecular network analysis and visualization
        to the community'
    note: null
    pmcid: PMC6821317
    pmid: '31074494'
    type:
    - Primary
    version: 12.2.3
  - doi: 10.1093/bib/bbz067
    metadata:
      abstract: The understanding of complex biological networks often relies on both
        a dedicated layout and a topology. Currently, there are three major competing
        layout-aware systems biology formats, but there are no software tools or software
        libraries supporting all of them. This complicates the management of molecular
        network layouts and hinders their reuse and extension. In this paper, we present
        a high-level overview of the layout formats in systems biology, focusing on
        their commonalities and differences, review their support in existing software
        tools, libraries and repositories and finally introduce a new conversion module
        within the MINERVA platform. The module is available via a REST API and offers,
        besides the ability to convert between layout-aware systems biology formats,
        the possibility to export layouts into several graphical formats. The module
        enables conversion of very large networks with thousands of elements, such
        as disease maps or metabolic reconstructions, rendering it widely applicable
        in systems biology.
      authors:
      - name: Hoksza D.
      - name: Gawron P.
      - name: Ostaszewski M.
      - name: Hasenauer J.
      - name: Schneider R.
      citationCount: 17
      date: '2019-07-10T00:00:00Z'
      journal: Briefings in Bioinformatics
      title: Closing the gap between formats for storing layout information in systems
        biology
    note: null
    pmcid: PMC7373180
    pmid: '31273380'
    type:
    - Primary
    version: 13.1.1
  - doi: 10.1089/big.2015.0057
    metadata:
      abstract: Translational medicine is a domain turning results of basic life science
        research into new tools and methods in a clinical environment, for example,
        as new diagnostics or therapies. Nowadays, the process of translation is supported
        by large amounts of heterogeneous data ranging from medical data to a whole
        range of -omics data. It is not only a great opportunity but also a great
        challenge, as translational medicine big data is difficult to integrate and
        analyze, and requires the involvement of biomedical experts for the data processing.
        We show here that visualization and interoperable workflows, combining multiple
        complex steps, can address at least parts of the challenge. In this article,
        we present an integrated workflow for exploring, analysis, and interpretation
        of translational medicine data in the context of human health. Three Web services
        - tranSMART, a Galaxy Server, and a MINERVA platform - are combined into one
        big data pipeline. Native visualization capabilities enable the biomedical
        experts to get a comprehensive overview and control over separate steps of
        the workflow. The capabilities of tranSMART enable a flexible filtering of
        multidimensional integrated data sets to create subsets suitable for downstream
        processing. A Galaxy Server offers visually aided construction of analytical
        pipelines, with the use of existing or custom components. A MINERVA platform
        supports the exploration of health and disease-related mechanisms in a contextualized
        analytical visualization system. We demonstrate the utility of our workflow
        by illustrating its subsequent steps using an existing data set, for which
        we propose a filtering scheme, an analytical pipeline, and a corresponding
        visualization of analytical results. The workflow is available as a sandbox
        environment, where readers can work with the described setup themselves. Overall,
        our work shows how visualization and interfacing of big data processing services
        facilitate exploration, analysis, and interpretation of translational medicine
        data.
      authors:
      - name: Satagopam V.
      - name: Gu W.
      - name: Eifes S.
      - name: Gawron P.
      - name: Ostaszewski M.
      - name: Gebel S.
      - name: Barbosa-Silva A.
      - name: Balling R.
      - name: Schneider R.
      citationCount: 39
      date: '2016-06-01T00:00:00Z'
      journal: Big Data
      title: Integration and Visualization of Translational Medicine Data for Better
        Understanding of Human Diseases
    note: null
    pmcid: PMC4932659
    pmid: '27441714'
    type:
    - Usage
    version: '10.0'
  - doi: 10.1016/j.envpol.2019.04.005
    metadata:
      abstract: 'Polychlorinated biphenyls (PCBs) are a class of widespread environmental
        pollutants, commonly found in human blood, that have been suggested to be
        linked to the occurrence of sporadic Parkinson''s disease (PD). It has been
        reported that some non-coplanar PCBs accumulate in the brains of female PD
        patients. To improve our understanding of the association between PCB exposure
        and PD risk we have applied whole transcriptome gene expression analysis in
        blood cells from 594 PCB-exposed subjects (369 female, 225 male). Interestingly,
        we observe that in females, blood levels of non-coplanar PCBs appear to be
        associated with expression levels of PD-specific genes. However, no such association
        was detected in males. Among the 131 PD-specific genes affected, 39 have been
        shown to display similar changes in expression levels in the substantia nigra
        of deceased PD patients. Especially among the down-regulated genes, transcripts
        of genes involved in neurotransmitter vesicle-related functions were predominant.
        Capsule: Plasma PCB levels are associated with gene expression changes in
        females only, resulting in brain-related genes changing in blood cells of
        healthy individuals exposed to PCBs.'
      authors:
      - name: Bohler S.
      - name: Krauskopf J.
      - name: Espin-Perez A.
      - name: Gebel S.
      - name: Palli D.
      - name: Rantakokko P.
      - name: Kiviranta H.
      - name: Kyrtopoulos S.A.
      - name: Balling R.
      - name: Kleinjans J.
      citationCount: 5
      date: '2019-07-01T00:00:00Z'
      journal: Environmental Pollution
      title: Genes associated with Parkinson's disease respond to increasing polychlorinated
        biphenyl levels in the blood of healthy females
    note: null
    pmcid: null
    pmid: '30991279'
    type: []
    version: 13.1.1
  relation:
  - biotoolsID: pathvisio
    type: uses
  - biotoolsID: sbgn
    type: uses
  - biotoolsID: libsbml
    type: uses
  toolType: []
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Translational medicine
    uri: http://edamontology.org/topic_3342
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 0
  version:
  - 13.1.3
  - 13.2.0
  - 14.0.13
  - 15.0.3
  - 16.4.0
  - 17.1.3
  - 18.1.1
- accessibility: Open access
  additionDate: '2025-06-25T13:31:29.384393Z'
  biotoolsCURIE: biotools:fantasiav2
  biotoolsID: fantasiav2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: fmpercan@upo.es
    fundrefid: null
    gridid: null
    name: Francisco Miguel Pérez Canales
    note: Programmer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    - Support
    - Provider
    url: http://www.bioinfocb.es/
  - email: a.rojas.m@csic.es
    fundrefid: null
    gridid: null
    name: Ana M Rojas Mendoza
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Contributor
    - Documentor
    - Support
    url: http://www.bioinfocb.es/
  - email: rosa.fernandez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Rosa Fernandez
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Documentor
    url: https://www.metazomics.com/
  - email: fraruimot@alum.us.es
    fundrefid: null
    gridid: null
    name: Francisco J. Ruiz Mota
    note: Junior developer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://www.bioinfocb.es/
  - email: gemma.martinez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Gemma Martinez Redondo
    note: Contributed  as developer of the first version of FANTASIA V1
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    url: https://www.metazomics.com/
  description: FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
    is a pipeline for protein annotating via GO term transference using the embedding
    space. FANTASIA’s latest developments include additional protein language models
    and provide enhanced functionalities.
  documentation:
  - note: Full documetnation with user cases, benchmarking, and cluster implementations
    type:
    - General
    url: https://fantasia.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors:
    - frapercan
    type: group
  elixirCommunity:
  - 3D-BioInfo
  - Proteomics
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output: []
  homepage: https://github.com/CBBIO/FANTASIA
  homepage_status: 0
  language:
  - Python
  - SQL
  lastUpdate: '2025-06-25T14:34:50.629045Z'
  license: MIT
  link:
  - note: Main repository contains documentation  from latest version
    type:
    - Repository
    url: https://github.com/CBBIO/FANTASIA
  - note: Main repository contains documentation  from linitial version based on Bioembeddings
      implementation.
    type:
    - Repository
    url: https://github.com/MetazoaPhylogenomicsLab/FANTASIA
  - note: Recommended tool for the Earth Biogenome Project
    type:
    - Software catalogue
    url: https://www.earthbiogenome.org/report-on-annotation-recommended-tools
  maturity: Mature
  name: FANTASIAV2
  operatingSystem:
  - Linux
  otherID: []
  owner: arojas
  publication:
  - doi: 10.1093/nargab/lqae078
    metadata:
      abstract: Protein language models have been tested and proved to be reliable
        when used on curated datasets but have not yet been applied to full proteomes.
        Accordingly, we tested how two different machine learning-based methods performed
        when decoding functional information from the proteomes of selected model
        organisms. We found that protein language models are more precise and informative
        than deep learning methods for all the species tested and across the three
        gene ontologies studied, and that they better recover functional information
        from transcriptomic experiments. The results obtained indicate that these
        language models are likely to be suitable for large-scale annotation and downstream
        analyses, and we recommend a guide for their use.
      authors:
      - name: Barrios-Nunez I.
      - name: Martinez-Redondo G.I.
      - name: Medina-Burgos P.
      - name: Cases I.
      - name: Fernandez R.
      - name: Rojas A.M.
      citationCount: 1
      date: '2024-09-01T00:00:00Z'
      journal: NAR Genomics and Bioinformatics
      title: Decoding functional proteome information in model organisms using protein
        language models
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  - doi: 10.1101/2024.02.28.582465
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Open science
    uri: http://edamontology.org/topic_4010
  validated: 0
  version:
  - 2.8.0
- accessibility: null
  additionDate: '2017-08-03T18:53:02Z'
  biotoolsCURIE: biotools:oncocnv
  biotoolsID: oncocnv
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: infos@oncodna.com
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.oncodna.com/
  - email: valentina.boeva@curie.fr
    fundrefid: null
    gridid: null
    name: Valentina Boeva
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Package to detect copy number changes in Deep Sequencing data developed
    by OncoDNA.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/BoevaLab/ONCOCNV/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  homepage: https://oncocnv.curie.fr/
  homepage_status: 0
  language:
  - R
  - Perl
  lastUpdate: '2025-06-25T13:52:15.437225Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/oncocnv-5-4-detection-of-copy-number-changes-in-deep-sequencing-data.html
  maturity: null
  name: ONCOCNV
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: aminoacid
  publication:
  - doi: 10.1093/bioinformatics/btu436
    metadata: null
    note: null
    pmcid: PMC4253825
    pmid: '25016581'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-04-08T08:17:22.895529Z'
  biotoolsCURIE: biotools:coreprofiler
  biotoolsID: coreprofiler
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: CoreProfiler is a cgMLST (core genome multilocus sequence typing) software
    that identifies alleles in bacterial genome assemblies by comparing them to a
    reference allele scheme. It detects both exact matches to known alleles and potential
    novel alleles using a two-step BLAST-based approach, enabling robust and reproducible
    strain genotyping.
  documentation:
  - note: null
    type:
    - General
    url: https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md?ref_type=heads
  download: []
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  - doi: 10.1016/S0022-2836(05)80360-2
    metadata:
      abstract: A new approach to rapid sequence comparison, basic local alignment
        search tool (BLAST), directly approximates alignments that optimize a measure
        of local similarity, the maximal segment pair (MSP) score. Recent mathematical
        results on the stochastic properties of MSP scores allow an analysis of the
        performance of this method as well as the statistical significance of alignments
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        in a number of ways and applied in a variety of contexts including straight-forward
        DNA and protein sequence database searches, motif searches, gene identification
        searches, and in the analysis of multiple regions of similarity in long DNA
        sequences. In addition to its flexibility and tractability to mathematical
        analysis, BLAST is an order of magnitude faster than existing sequence comparison
        tools of comparable sensitivity. © 1990, Academic Press Limited. All rights
        reserved.
      authors:
      - name: Altschul S.F.
      - name: Gish W.
      - name: Miller W.
      - name: Myers E.W.
      - name: Lipman D.J.
      citationCount: 80157
      date: '1990-01-01T00:00:00Z'
      journal: Journal of Molecular Biology
      title: Basic local alignment search tool
    note: null
    pmcid: null
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    type: []
    version: null
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  topic:
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  - term: Bioinformatics
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  - term: Phylogenetics
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  description: AutoDock Vina is a new open-source program for drug discovery, molecular
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  - note: null
    type:
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  description: An online implementation of Cytoscape Desktop that captures its interface
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  function:
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    operation:
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    - term: Protein interaction network analysis
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    - term: Pathway or network comparison
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    type:
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  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Bioinformatics
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  - term: Imaging
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- accessibility: Open access
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    note: null
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    rorid: null
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    url: null
  - email: pierluigi.martelli@unibo.it
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    name: Pier Luigi Martelli
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    rorid: null
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    url: http://biocomp.unibo.it
  description: Prediction of secretory signal peptides in protein sequences
  documentation:
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    type:
    - Command-line options
    url: https://github.com/BolognaBiocomp/deepsig
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    type: Container file
    url: https://hub.docker.com/r/bolognabiocomp/deepsig
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  function:
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    input:
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        term: Protein sequence (raw)
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      format:
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    - data:
        term: Taxonomy
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      format:
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        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Protein signal peptide detection
      uri: http://edamontology.org/operation_0418
    output:
    - data:
        term: Protein report
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      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://busca.biocomp.unibo.it/deepsig/
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2025-06-19T11:55:09.017105Z'
  license: GPL-3.0
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  name: DeepSig
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  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btx818
    metadata:
      abstract: Motivation The identification of signal peptides in protein sequences
        is an important step toward protein localization and function characterization.
        Results Here, we present DeepSig, an improved approach for signal peptide
        detection and cleavage-site prediction based on deep learning methods. Comparative
        benchmarks performed on an updated independent dataset of proteins show that
        DeepSig is the current best performing method, scoring better than other available
        state-of-the-art approaches on both signal peptide detection and precise cleavage-site
        identification. Availability and implementation DeepSig is available as both
        standalone program and web server at https://deepsig.biocomp.unibo.it. All
        datasets used in this study can be obtained from the same website.
      authors:
      - name: Savojardo C.
      - name: Martelli P.L.
      - name: Fariselli P.
      - name: Casadio R.
      citationCount: 96
      date: '2018-05-15T00:00:00Z'
      journal: Bioinformatics
      title: 'DeepSig: Deep learning improves signal peptide detection in proteins'
    note: null
    pmcid: PMC5946842
    pmid: '29280997'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version:
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- accessibility: null
  additionDate: '2025-05-22T12:06:46.866961Z'
  biotoolsCURIE: biotools:breast_dense_tissue_segmentation
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  credit: []
  description: The tool takes a digital mammogram and performs an automatic segmentation
    of the breast area and the dense tissue. After the mammogram segmentation, the
    tool returns a DICOM-SEG image with both the dense tissue and the breast tissue
    mask combined.
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  function:
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    operation:
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  homepage: https://pubmed.ncbi.nlm.nih.gov/36010173/
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  license: Proprietary
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  name: Breast Dense Tissue Segmentation
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  owner: dsilveira
  publication:
  - doi: 10.3390/diagnostics12081822
    metadata:
      abstract: Breast density assessed from digital mammograms is a known biomarker
        related to a higher risk of developing breast cancer. Supervised learning
        algorithms have been implemented to determine this. However, the performance
        of these algorithms depends on the quality of the ground-truth information,
        which expert readers usually provide. These expert labels are noisy approximations
        to the ground truth, as there is both intra- and inter-observer variability
        among them. Thus, it is crucial to provide a reliable method to measure breast
        density from mammograms. This paper presents a fully automated method based
        on deep learning to estimate breast density, including breast detection, pectoral
        muscle exclusion, and dense tissue segmentation. We propose a novel confusion
        matrix (CM)—YNet model for the segmentation step. This architecture includes
        networks to model each radiologist’s noisy label and gives the estimated ground-truth
        segmentation as well as two parameters that allow interaction with a threshold-based
        labeling tool. A multi-center study involving 1785 women whose “for presentation”
        mammograms were obtained from 11 different medical facilities was performed.
        A total of 2496 mammograms were used as the training corpus, and 844 formed
        the testing corpus. Additionally, we included a totally independent dataset
        from a different center, composed of 381 women with one image per patient.
        Each mammogram was labeled independently by two expert radiologists using
        a threshold-based tool. The implemented CM-Ynet model achieved the highest
        DICE score averaged over both test datasets (0.82 ± 0.14) when compared to
        the closest dense-tissue segmentation assessment from both radiologists. The
        level of concordance between the two radiologists showed a DICE score of (0.76
        ± 0.17). An automatic breast density estimator based on deep learning exhibited
        higher performance when compared with two experienced radiologists. This suggests
        that modeling each radiologist’s label allows for better estimation of the
        unknown ground-truth segmentation. The advantage of the proposed model is
        that it also provides the threshold parameters that enable user interaction
        with a threshold-based tool.
      authors:
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      - name: Perez-Benito F.J.
      - name: Perez-Cortes J.-C.
      - name: Roman M.
      - name: Pollan M.
      - name: Perez-Gomez B.
      - name: Salas-Trejo D.
      - name: Casals M.
      - name: Llobet R.
      citationCount: 5
      date: '2022-08-01T00:00:00Z'
      journal: Diagnostics
      title: 'Breast Dense Tissue Segmentation with Noisy Labels: A Hybrid Threshold-Based
        and Mask-Based Approach'
    note: null
    pmcid: PMC9406546
    pmid: '36010173'
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
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  biotoolsCURIE: biotools:extended_a_priori_probability_tool
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  credit: []
  description: The tool provides a semi-supervised metric (EAPP) for binary classification
    tasks that considers not only the a priori probability but also some possible
    bias present in the dataset, as well as other features that could provide a relatively
    trivial separability of the target classes. Therefore, it allows for evaluating
    the ease or complexity of the task or bias of the data beyond the well-established
    baseline for any binary classification.
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    operation:
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  homepage: https://ieeexplore.ieee.org/document/9950248
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  lastUpdate: '2025-06-19T06:22:40.072300Z'
  license: Proprietary
  link: []
  maturity: null
  name: EAPP - Extended a Priori Probability tool
  operatingSystem: []
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  owner: dsilveira
  publication:
  - doi: 10.1109/ACCESS.2022.3221936
    metadata:
      abstract: The a priori probability of a dataset is usually used as a baseline
        for comparing a particular algorithm's accuracy in a given binary classification
        task. ZeroR is the simplest algorithm for this, predicting the majority class
        for all examples. However, this is an extremely simple approach that has no
        predictive power and does not describe other dataset features that could lead
        to a more demanding baseline. In this paper, we present the Extended A Priori
        Probability (EAPP), a novel semi-supervised baseline metric for binary classification
        tasks that considers not only the a priori probability but also some possible
        bias present in the dataset as well as other features that could provide a
        relatively trivial separability of the target classes. The approach is based
        on the area under the ROC curve (AUC ROC), known to be quite insensitive to
        class imbalance. The procedure involves multiobjective feature extraction
        and a clustering stage in the input space with autoencoders and a subsequent
        combinatory weighted assignation from clusters to classes depending on the
        distance to nearest clusters for each class. Class labels are then assigned
        to establish the combination that maximizes AUC ROC for each number of clusters
        considered. To avoid overfit in the combined feature extraction and clustering
        method, a cross-validation scheme is performed in each case. EAPP is defined
        for different numbers of clusters, starting from the inverse of the minority
        class proportion, which is useful for a fair comparison among diversely imbalanced
        datasets. A high EAPP usually relates to an easy binary classification task,
        but it also may be due to a significant coarse-grained bias in the dataset,
        when the task is previously known to be difficult. This metric represents
        a baseline beyond the a priori probability to assess the actual capabilities
        of binary classification models.
      authors:
      - name: Castello V.O.
      - name: Perez-Benito F.J.
      - name: Catala O.D.T.
      - name: Igual I.S.
      - name: Llobet R.
      - name: Perez-Cortes J.-C.
      citationCount: 0
      date: '2022-01-01T00:00:00Z'
      journal: IEEE Access
      title: 'Extended a Priori Probability (EAPP): A Data-Driven Approach for Machine
        Learning Binary Classification Tasks'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 0
  version:
  - v1.0.1
- accessibility: Open access
  additionDate: '2021-05-27T09:02:10Z'
  biotoolsCURIE: biotools:qiime2
  biotoolsID: qiime2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: greg.caporaso@nau.edu
    fundrefid: null
    gridid: null
    name: Greg Caporaso
    note: null
    orcidid: https://orcid.org/0000-0002-8865-1670
    rorid: null
    typeEntity: null
    typeRole:
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    url: https://cap-lab.bio
  description: QIIME 2 is an AI-ready microbiome multi-omics data science platform
    that is trusted, free, open source, extensible, and community developed and supported
    bioinformatics.
  documentation:
  - note: User documentation for amplicon analysis, oriented to new users.
    type:
    - General
    url: https://amplicon-docs.qiime2.org
  - note: User documentation for metagenome analysis, oriented to new users.
    type:
    - Installation instructions
    url: https://moshpit.qiime2.org
  - note: User documentation, oriented toward power users.
    type:
    - User manual
    url: https://use.qiime2.org
  - note: Developer documentation, including a plugin development tutorial.
    type:
    - API documentation
    url: https://develop.qiime2.org
  - note: 'The QIIME 2 Library Stacks: a resource for discovering relevant documentation.'
    type:
    - Other
    url: https://library.qiime2.org/books
  download: []
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  function:
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    input: []
    note: null
    operation:
    - term: Demultiplexing
      uri: http://edamontology.org/operation_3933
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output: []
  homepage: https://qiime2.org
  homepage_status: 0
  language:
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  lastUpdate: '2025-06-18T21:00:46.185472Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/qiime2
  - note: null
    type:
    - Software catalogue
    url: https://library.qiime2.org
  - note: null
    type:
    - Discussion forum
    url: https://forum.qiime2.org
  - note: Site for viewing and interacting with QIIME 2 results.
    type:
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    url: https://view.qiime2.org
  maturity: Mature
  name: QIIME 2
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: gregcaporaso
  publication:
  - doi: 10.1038/s41587-019-0209-9
    metadata:
      abstract: ''
      authors:
      - name: Bolyen E.
      - name: Rideout J.R.
      - name: Dillon M.R.
      - name: Bokulich N.A.
      - name: Abnet C.C.
      - name: Al-Ghalith G.A.
      - name: Alexander H.
      - name: Alm E.J.
      - name: Arumugam M.
      - name: Asnicar F.
      - name: Bai Y.
      - name: Bisanz J.E.
      - name: Bittinger K.
      - name: Brejnrod A.
      - name: Brislawn C.J.
      - name: Brown C.T.
      - name: Callahan B.J.
      - name: Caraballo-Rodriguez A.M.
      - name: Chase J.
      - name: Cope E.K.
      - name: Da Silva R.
      - name: Diener C.
      - name: Dorrestein P.C.
      - name: Douglas G.M.
      - name: Durall D.M.
      - name: Duvallet C.
      - name: Edwardson C.F.
      - name: Ernst M.
      - name: Estaki M.
      - name: Fouquier J.
      - name: Gauglitz J.M.
      - name: Gibbons S.M.
      - name: Gibson D.L.
      - name: Gonzalez A.
      - name: Gorlick K.
      - name: Guo J.
      - name: Hillmann B.
      - name: Holmes S.
      - name: Holste H.
      - name: Huttenhower C.
      - name: Huttley G.A.
      - name: Janssen S.
      - name: Jarmusch A.K.
      - name: Jiang L.
      - name: Kaehler B.D.
      - name: Kang K.B.
      - name: Keefe C.R.
      - name: Keim P.
      - name: Kelley S.T.
      - name: Knights D.
      - name: Koester I.
      - name: Kosciolek T.
      - name: Kreps J.
      - name: Langille M.G.I.
      - name: Lee J.
      - name: Ley R.
      - name: Liu Y.-X.
      - name: Loftfield E.
      - name: Lozupone C.
      - name: Maher M.
      - name: Marotz C.
      - name: Martin B.D.
      - name: McDonald D.
      - name: McIver L.J.
      - name: Melnik A.V.
      - name: Metcalf J.L.
      - name: Morgan S.C.
      - name: Morton J.T.
      - name: Naimey A.T.
      - name: Navas-Molina J.A.
      - name: Nothias L.F.
      - name: Orchanian S.B.
      - name: Pearson T.
      - name: Peoples S.L.
      - name: Petras D.
      - name: Preuss M.L.
      - name: Pruesse E.
      - name: Rasmussen L.B.
      - name: Rivers A.
      - name: Robeson M.S.
      - name: Rosenthal P.
      - name: Segata N.
      - name: Shaffer M.
      - name: Shiffer A.
      - name: Sinha R.
      - name: Song S.J.
      - name: Spear J.R.
      - name: Swafford A.D.
      - name: Thompson L.R.
      - name: Torres P.J.
      - name: Trinh P.
      - name: Tripathi A.
      - name: Turnbaugh P.J.
      - name: Ul-Hasan S.
      - name: van der Hooft J.J.J.
      - name: Vargas F.
      - name: Vazquez-Baeza Y.
      - name: Vogtmann E.
      - name: von Hippel M.
      - name: Walters W.
      - name: Wan Y.
      - name: Wang M.
      - name: Warren J.
      - name: Weber K.C.
      - name: Williamson C.H.D.
      - name: Willis A.D.
      - name: Xu Z.Z.
      - name: Zaneveld J.R.
      - name: Zhang Y.
      - name: Zhu Q.
      - name: Knight R.
      - name: Caporaso J.G.
      citationCount: 14289
      date: '2019-08-01T00:00:00Z'
      journal: Nature Biotechnology
      title: Reproducible, interactive, scalable and extensible microbiome data science
        using QIIME 2
    note: null
    pmcid: PMC7015180
    pmid: '31341288'
    type:
    - Primary
    version: '2.0'
  relation:
  - biotoolsID: qiime
    type: isNewVersionOf
  toolType:
  - Suite
  - Command-line tool
  - Library
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Metatranscriptomics
    uri: http://edamontology.org/topic_3941
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2025-06-17T20:53:54.551980Z'
  biotoolsCURIE: biotools:metasbt
  biotoolsID: metasbt
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: fabio.cumbo@gmail.com
    fundrefid: null
    gridid: null
    name: Fabio Cumbo
    note: null
    orcidid: https://orcid.org/0000-0003-2920-5838
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    - Support
    url: https://cumbof.github.io
  description: MetaSBT is a scalable framework designed to automatically index microbial
    genomes and accurately characterize metagenome-assembled genomes using Sequence
    Bloom Trees.
  documentation:
  - note: Official MetaSBT Wiki
    type:
    - General
    url: https://github.com/cumbof/MetaSBT/wiki
  download:
  - note: null
    type: Software package
    url: https://pypi.io/packages/source/m/metasbt/metasbt-0.1.4.post1.tar.gz
    version: 0.1.4
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/cumbof/MetaSBT
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-18T17:12:50.842659Z'
  license: MIT
  link:
  - note: Framework Repository
    type:
    - Repository
    url: https://github.com/cumbof/MetaSBT
  - note: Repository with Public MetaSBT Databases
    type:
    - Repository
    url: https://github.com/cumbof/MetaSBT-DBs
  maturity: Mature
  name: MetaSBT
  operatingSystem:
  - Linux
  otherID: []
  owner: fabiocumbo
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - 0.1.4.post1
- accessibility: Open access (with restrictions)
  additionDate: '2021-07-06T20:27:27Z'
  biotoolsCURIE: biotools:nanoplot
  biotoolsID: nanoplot
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Wouter De Coster
    note: null
    orcidid: https://orcid.org/0000-0002-5248-8197
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://gigabaseorgigabyte.wordpress.com/
  description: NanoPlot is a tool with various visualizations of sequencing data in
    bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for
    long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://github.com/wdecoster/NanoPlot
  download:
  - note: null
    type: Command-line specification
    url: https://anaconda.org/bioconda/nanoplot
    version: null
  - note: null
    type: Command-line specification
    url: https://pypi.org/project/NanoPlot/
    version: null
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    note: null
    operation:
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Box-Whisker plot plotting
      uri: http://edamontology.org/operation_2943
    output: []
  homepage: https://github.com/wdecoster/NanoPlot
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-18T12:31:48.762608Z'
  license: GPL-3.0
  link:
  - note: Issue tracker and most up to date software version
    type:
    - Repository
    url: https://github.com/wdecoster/NanoPlot
  - note: Web service with more limited options compared to the command line tool
    type:
    - Service
    url: http://nanoplot.bioinf.be/
  maturity: Mature
  name: NanoPlot
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: wdecoster
  publication:
  - doi: 10.1093/bioinformatics/bty149
    metadata:
      abstract: 'Summary: Here we describe NanoPack, a set of tools developed for
        visualization and processing of long-read sequencing data from Oxford Nanopore
        Technologies and Pacific Biosciences. Availability and implementation: The
        NanoPack tools are written in Python3 and released under the GNU GPL3.0 License.
        The source code can be found at https://github.com/wdecoster/nanopack, together
        with links to separate scripts and their documentation. The scripts are compatible
        with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available
        as a graphical user interface, a web service at http://nanoplot.bioinf.be
        and command line tools.'
      authors:
      - name: De Coster W.
      - name: D'Hert S.
      - name: Schultz D.T.
      - name: Cruts M.
      - name: Van Broeckhoven C.
      citationCount: 1840
      date: '2018-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'NanoPack: Visualizing and processing long-read sequencing data'
    note: null
    pmcid: PMC6061794
    pmid: '29547981'
    type:
    - Method
    version: null
  relation:
  - biotoolsID: nanopack
    type: includedIn
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - v.1.42.0
- accessibility: Open access
  additionDate: '2019-09-13T12:51:16Z'
  biotoolsCURIE: biotools:kraken2
  biotoolsID: kraken2
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Derrick E. Wood
    note: null
    orcidid: http://orcid.org/0000-0002-7429-1854
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jennifer Lu
    note: null
    orcidid: http://orcid.org/0000-0001-9167-2002
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: langmea@cs.jhu.edu
    fundrefid: null
    gridid: null
    name: Ben Langmead
    note: null
    orcidid: http://orcid.org/0000-0003-2437-1976
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Kraken 2 is the newest version of Kraken, a taxonomic classification
    system using exact k-mer matches to achieve high accuracy and fast classification
    speeds. This classifier matches each k-mer within a query sequence to the lowest
    common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments
    inform the classification algorithm.

    Any assumption that Kraken’s raw read assignments can be directly translated into
    species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation
    of Abundance after Classification with KrakEN), estimates species abundances in
    metagenomics samples by probabilistically re-distributing reads in the taxonomic
    tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics
    data.”)'
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/DerrickWood/kraken2/wiki/Manual
  - note: Links to multiple Kraken 2 and bracken databases and indexes
    type:
    - User manual
    url: https://benlangmead.github.io/aws-indexes/k2
  download:
  - note: null
    type: Source code
    url: https://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gz
    version: 2.0.8-beta
  editPermission:
    authors:
    - vashokan
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: '`kraken2 --db <kraken2_database> <input.fastq>`'
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://ccb.jhu.edu/software/kraken2/
  homepage_status: 0
  language:
  - C++
  - Perl
  lastUpdate: '2025-06-18T12:24:26.657325Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/DerrickWood/kraken2
  - note: null
    type:
    - Issue tracker
    url: https://github.com/DerrickWood/kraken2/issues
  maturity: null
  name: kraken2
  operatingSystem: []
  otherID: []
  owner: anand-anshu
  publication:
  - doi: 10.1101/762302
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: kraken
    type: isNewVersionOf
  - biotoolsID: bracken
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  validated: 1
  version:
  - 2.0.8-beta
- accessibility: null
  additionDate: '2018-07-01T13:17:42Z'
  biotoolsCURIE: biotools:nanopack
  biotoolsID: nanopack
  collectionID:
  - VIB
  confidence_flag: null
  cost: null
  credit:
  - email: wouter.decoster@molgen.vib-ua.be
    fundrefid: null
    gridid: null
    name: Wouter De Coster
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Visualizing and processing long-read sequencing data.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/wdecoster/nanopack
  download: []
  editPermission:
    authors:
    - bits@vib.be
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output: []
  homepage: https://github.com/wdecoster/nanopack
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-18T12:21:28.393467Z'
  license: null
  link: []
  maturity: null
  name: NanoPack
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.1093/bioinformatics/bty149
    metadata:
      abstract: 'Summary: Here we describe NanoPack, a set of tools developed for
        visualization and processing of long-read sequencing data from Oxford Nanopore
        Technologies and Pacific Biosciences. Availability and implementation: The
        NanoPack tools are written in Python3 and released under the GNU GPL3.0 License.
        The source code can be found at https://github.com/wdecoster/nanopack, together
        with links to separate scripts and their documentation. The scripts are compatible
        with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available
        as a graphical user interface, a web service at http://nanoplot.bioinf.be
        and command line tools.'
      authors:
      - name: De Coster W.
      - name: D'Hert S.
      - name: Schultz D.T.
      - name: Cruts M.
      - name: Van Broeckhoven C.
      citationCount: 1840
      date: '2018-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'NanoPack: Visualizing and processing long-read sequencing data'
    note: null
    pmcid: PMC6061794
    pmid: '29547981'
    type: []
    version: null
  relation:
  - biotoolsID: nanoplot
    type: includes
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 1.1.0
- accessibility: Open access
  additionDate: '2021-05-26T21:13:32Z'
  biotoolsCURIE: biotools:nextdenovo
  biotoolsID: nextdenovo
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: support@nextomics.org
    fundrefid: null
    gridid: null
    name: Nextomics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Primary contact
    url: null
  description: NextDenovo is a string graph-based de novo assembler for long reads
    (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu
    (no correction step for PacBio Hifi reads), but requires significantly less computing
    resources and storages.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nextdenovo.readthedocs.io/en/latest/
  download:
  - note: null
    type: Source code
    url: https://github.com/Nextomics/NextDenovo/releases/tag/2.5.2
    version: null
  editPermission:
    authors:
    - jw
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    output:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: Sequence assembly format (text)
        uri: http://edamontology.org/format_2561
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Nextomics/NextDenovo
  homepage_status: 0
  language:
  - Python
  - C
  lastUpdate: '2025-06-18T12:20:23.607241Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/Nextomics/NextDenovo/issues
  maturity: Mature
  name: NextDenovo
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1101/2023.03.09.531669.
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - v.2.5.2
- accessibility: Open access
  additionDate: '2021-05-27T09:04:45Z'
  biotoolsCURIE: biotools:quickmerge
  biotoolsID: quickmerge
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Mahul Chakraborty
    note: null
    orcidid: https://orcid.org/0000-0003-2414-9187
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://mahulchakraborty.wordpress.com/
  description: Quickmerge is a program that uses complementary information from genomes
    assembled with long reads in order to improve contiguity, and works with assemblies
    derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even
    work with hybrid assemblies made by combining long reads and Illumina short reads.
  documentation: []
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: merge_wrapper.py -pre output_prefix assembly_1.fa assembly_2.fa
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: 'Runs whole merge process on an input assembly.

      Assembly 2 will be used to fill gaps in assembly 1.'
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/mahulchak/quickmerge
  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2025-06-18T12:17:20.983962Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/mahulchak/quickmerge/issues
  - note: null
    type:
    - Repository
    url: https://github.com/mahulchak/quickmerge
  maturity: null
  name: quickmerge
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1534/g3.118.200162
    metadata:
      abstract: Accurate and comprehensive characterization of genetic variation is
        essential for deciphering the genetic basis of diseases and other phenotypes.
        A vast amount of genetic variation stems from largescale sequence changes
        arising from the duplication, deletion, inversion, and translocation of sequences.
        In the past 10 years, high-throughput short reads have greatly expanded our
        ability to assay sequence variation due to single nucleotide polymorphisms.
        However, a recent de novo assembly of a second Drosophila melanogaster reference
        genome has revealed that short read genotyping methods miss hundreds of structural
        variants, including those affecting phenotypes. While genomes assembled using
        highcoverage long reads can achieve high levels of contiguity and completeness,
        concerns about cost, errors, and low yield have limited widespread adoption
        of such sequencing approaches. Here we resequenced the reference strain of
        D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for
        24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we
        assembled a highly contiguous de novo genome. The addition of inexpensive
        paired reads and subsequent scaffolding using an optical map technology achieved
        an assembly with completeness and contiguity comparable to the D. melanogaster
        reference assembly. Comparison of our assembly to the reference assembly of
        ISO1 uncovered a number of structural variants (SVs), including novel LTR
        transposable element insertions and duplications affecting genes with developmental,
        behavioral, and metabolic functions. Collectively, these SVs provide a snapshot
        of the dynamics of genome evolution. Furthermore, our assembly and comparison
        to the D. melanogaster reference genome demonstrates that high-quality de
        novo assembly of reference genomes and comprehensive variant discovery using
        such assemblies are now possible by a single lab for under $1,000 (USD).
      authors:
      - name: Solares E.A.
      - name: Chakraborty M.
      - name: Miller D.E.
      - name: Kalsow S.
      - name: Hall K.
      - name: Perera A.G.
      - name: Emerson J.J.
      - name: Scott Hawley R.
      citationCount: 70
      date: '2018-10-01T00:00:00Z'
      journal: 'G3: Genes, Genomes, Genetics'
      title: Rapid low-cost assembly of the drosophila melanogaster reference genome
        using low-coverage, long-read sequencing
    note: null
    pmcid: PMC6169397
    pmid: '30018084'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version:
  - v.0.3
- accessibility: Open access
  additionDate: '2022-05-16T13:26:15.720803Z'
  biotoolsCURIE: biotools:skm
  biotoolsID: skm
  collectionID:
  - ELIXIR-SI
  - Plant Systems Biology
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: National Institute of Biology, Department of Biotechnology and Systems Biology
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: http://www.nib.si/
  - email: carissarobyn.bleker@nib.si
    fundrefid: null
    gridid: null
    name: Carissa Bleker
    note: null
    orcidid: https://orcid.org/0000-0003-1617-7145
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kristina Gruden
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Živa Ramšak
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vid Podpečan
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: 'Stress Knowledge Map:  A compilation of knowledge on mechanisms underlying
    responses of plants to stress, the so called stress signalling network.'
  documentation:
  - note: null
    type:
    - General
    url: https://skm.nib.si/documentation
  download: []
  editPermission:
    authors:
    - zagor
    type: group
  elixirCommunity:
  - Plant Sciences
  elixirNode:
  - Slovenia
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene name
        uri: http://edamontology.org/data_2299
      format: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: sif
        uri: http://edamontology.org/format_3619
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Mathematical model
        uri: http://edamontology.org/data_0950
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: SBGN-ML
        uri: http://edamontology.org/format_3692
      - term: sif
        uri: http://edamontology.org/format_3619
  homepage: https://skm.nib.si/
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-18T12:10:26.465410Z'
  license: null
  link:
  - note: null
    type:
    - Other
    url: https://skm.nib.si/contact
  maturity: Emerging
  name: SKM
  operatingSystem: []
  otherID: []
  owner: carissa
  publication:
  - doi: 10.1016/j.xplc.2024.100920
    metadata:
      abstract: 'Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available
        resource containing two complementary knowledge graphs that describe the current
        knowledge of biochemical, signaling, and regulatory molecular interactions
        in plants: a highly curated model of plant stress signaling (PSS; 543 reactions)
        and a large comprehensive knowledge network (488 390 interactions). Both were
        constructed by domain experts through systematic curation of diverse literature
        and database resources. SKM provides a single entry point for investigations
        of plant stress response and related growth trade-offs, as well as interactive
        explorations of current knowledge. PSS is also formulated as a qualitative
        and quantitative model for systems biology and thus represents a starting
        point for a plant digital twin. Here, we describe the features of SKM and
        show, through two case studies, how it can be used for complex analyses, including
        systematic hypothesis generation and design of validation experiments, or
        to gain new insights into experimental observations in plant biology.'
      authors:
      - name: Bleker C.
      - name: Ramsak
      - name: Bittner A.
      - name: Podpecan V.
      - name: Zagorscak M.
      - name: Wurzinger B.
      - name: Baebler
      - name: Petek M.
      - name: Kriznik M.
      - name: van Dieren A.
      - name: Gruber J.
      - name: Afjehi-Sadat L.
      - name: Weckwerth W.
      - name: Zupanic A.
      - name: Teige M.
      - name: Vothknecht U.C.
      - name: Gruden K.
      citationCount: 8
      date: '2024-06-10T00:00:00Z'
      journal: Plant Communications
      title: 'Stress Knowledge Map: A knowledge graph resource for systems biology
        analysis of plant stress responses'
    note: 'Stress Knowledge Map: A knowledge graph resource for systems biology analysis
      of plant stress responses'
    pmcid: null
    pmid: '38616489'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: gomapman
    type: uses
  - biotoolsID: newt-ve
    type: uses
  toolType:
  - Web application
  - Database portal
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2025-06-18T11:53:52.861712Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ablab/quast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: Open access
  additionDate: '2019-11-14T18:44:38Z'
  biotoolsCURIE: biotools:Racon
  biotoolsID: Racon
  collectionID:
  - ONTeater
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: cskang@korea.kr
    fundrefid: null
    gridid: null
    name: Chon-Sik Kang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: changsookim@cnu.ac.kr
    fundrefid: null
    gridid: null
    name: Changsoo Kim
    note: null
    orcidid: https://orcid.org/0000-0002-3596-2934
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Consensus module for raw de novo DNA assembly of long uncorrected
    reads


    Racon is intended as a standalone consensus module to correct raw contigs generated
    by rapid assembly methods which do not include a consensus step. The goal of Racon
    is to generate genomic consensus which is of similar or better quality compared
    to the output generated by assembly methods which employ both error correction
    and consensus steps, while providing a speedup of several times compared to those
    methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore
    Technologies.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: racon -u reads.fa mapped_reads.sam assembly.fa > assembly_racon.fa
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# The mapping file can be generated with any mapping program - eg, bwa-mem
      or minimap2.

      # The following is an example using minimap2 with ONT data

      minimap2 assembly.fa-ax map-ont reads.fa > mapped_reads.sam'
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Mapping assembly
      uri: http://edamontology.org/operation_0523
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/isovic/racon
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2025-06-18T11:42:42.378216Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/isovic/racon
  - note: null
    type:
    - Issue tracker
    url: https://github.com/isovic/racon/issues
  maturity: null
  name: Racon
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.3390/plants8080270
    metadata:
      abstract: 'The whole genome sequencing (WGS) has become a crucial tool in understanding
        genome structure and genetic variation. The MinION sequencing of Oxford Nanopore
        Technologies (ONT) is an excellent approach for performing WGS and it has
        advantages in comparison with other Next-Generation Sequencing (NGS): It is
        relatively inexpensive, portable, has simple library preparation, can be monitored
        in real-time, and has no theoretical limits on reading length. Sorghum bicolor
        (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb,
        and its genome sequence information is released in the Phytozome database.
        Therefore, sorghum can be used as a good reference. However, plant species
        have complex and large genomes when compared to animals or microorganisms.
        As a result, complete genome sequencing is difficult for plant species. MinION
        sequencing that produces long-reads can be an excellent tool for overcoming
        the weak assembly of short-reads generated from NGS by minimizing the generation
        of gaps or covering the repetitive sequence that appears on the plant genome.
        Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using
        the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca.
        25× coverage of reference) from long-read sequence data. A total of 6124 contigs
        (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering
        50%) were generated from Minimap and Miniasm with a Racon through a de novo
        assembly using two different tools and mapped assembled contigs against the
        sorghum reference genome. Our results provide an optimal series of long-read
        sequencing analysis for plant species while using the MinION platform and
        a clue to determine the total sequencing scale for optimal coverage that is
        based on various genome sizes.'
      authors:
      - name: Lee Y.G.
      - name: Choi S.C.
      - name: Kang Y.
      - name: Kim K.M.
      - name: Kang C.-S.
      - name: Kim C.
      citationCount: 13
      date: '2019-08-01T00:00:00Z'
      journal: Plants
      title: 'Constructing a reference genome in a single lab: The possibility to
        use oxford nanopore technology'
    note: null
    pmcid: PMC6724115
    pmid: '31390788'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-11-14T20:08:20Z'
  biotoolsCURIE: biotools:Flye
  biotoolsID: Flye
  collectionID:
  - ONTeater
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: fenderglass@gmail.com
    fundrefid: null
    gridid: null
    name: Mikhail Kolmogorov
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Yu Lin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jeffrey Yuan
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'Flye is a de novo assembler for single molecule sequencing reads,
    such as those produced by PacBio and Oxford Nanopore Technologies. It is designed
    for a wide range of datasets, from small bacterial projects to large mammalian-scale
    assemblies. The package represents a complete pipeline: it takes raw PB / ONT
    reads as input and outputs polished contigs.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Mapping assembly
      uri: http://edamontology.org/operation_0523
    - term: Cross-assembly
      uri: http://edamontology.org/operation_3730
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/fenderglass/Flye
  homepage_status: 0
  language:
  - C++
  - Python
  - C
  lastUpdate: '2025-06-18T10:20:03.775603Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/fenderglass/Flye/issues
  - note: null
    type:
    - Repository
    url: https://github.com/mikolmogorov/Flye
  maturity: null
  name: Flye
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1099/mgen.0.000294
    metadata:
      abstract: Illumina sequencing allows rapid, cheap and accurate whole genome
        bacterial analyses, but short reads (<300 bp) do not usually enable complete
        genome assembly. Long-read sequencing greatly assists with resolving complex
        bacterial genomes, particularly when combined with short-read Illumina data
        (hybrid assembly). However, it is not clear how different long-read sequencing
        methods affect hybrid assembly accuracy. Relative automation of the assembly
        process is also crucial to facilitating high-throughput complete bacterial
        genome reconstruction, avoiding multiple bespoke filtering and data manipulation
        steps. In this study, we compared hybrid assemblies for 20 bacterial isolates,
        including two reference strains, using Illumina sequencing and long reads
        from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences
        (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae,
        as these frequently have highly plastic, repetitive genetic structures, and
        complete genome reconstruction for these species is relevant for a precise
        understanding of the epidemiology of antimicrobial resistance. We de novo
        assembled genomes using the hybrid assembler Unicycler and compared different
        read processing strategies, as well as comparing to long-read-only assembly
        with Flye followed by short-read polishing with Pilon. Hybrid assembly with
        either PacBio or ONT reads facilitated high-quality genome reconstruction,
        and was superior to the longread assembly and polishing approach evaluated
        with respect to accuracy and completeness. Combining ONT and Illumina reads
        fully resolved most genomes without additional manual steps, and at a lower
        consumables cost per isolate in our setting. Automated hybrid assembly is
        a powerful tool for complete and accurate bacterial genome assembly.
      authors:
      - name: De Maio N.
      - name: Shaw L.P.
      - name: Hubbard A.
      - name: George S.
      - name: Sanderson N.D.
      - name: Swann J.
      - name: Wick R.
      - name: Oun M.A.
      - name: Stubberfield E.
      - name: Hoosdally S.J.
      - name: Crook D.W.
      - name: Peto T.E.A.
      - name: Sheppard A.E.
      - name: Bailey M.J.
      - name: Read D.S.
      - name: Anjum M.F.
      - name: Sarah Walker A.
      - name: Stoesser N.
      citationCount: 166
      date: '2019-01-01T00:00:00Z'
      journal: Microbial Genomics
      title: Comparison of long-read sequencing technologies in the hybrid assembly
        of complex bacterial genomes
    note: null
    pmcid: PMC6807382
    pmid: '31483244'
    type:
    - Usage
    version: null
  - doi: 10.1038/s41587-019-0072-8
    metadata:
      abstract: Accurate genome assembly is hampered by repetitive regions. Although
        long single molecule sequencing reads are better able to resolve genomic repeats
        than short-read data, most long-read assembly algorithms do not provide the
        repeat characterization necessary for producing optimal assemblies. Here,
        we present Flye, a long-read assembly algorithm that generates arbitrary paths
        in an unknown repeat graph, called disjointigs, and constructs an accurate
        repeat graph from these error-riddled disjointigs. We benchmark Flye against
        five state-of-the-art assemblers and show that it generates better or comparable
        assemblies, while being an order of magnitude faster. Flye nearly doubled
        the contiguity of the human genome assembly (as measured by the NGA50 assembly
        quality metric) compared with existing assemblers.
      authors:
      - name: Kolmogorov M.
      - name: Yuan J.
      - name: Lin Y.
      - name: Pevzner P.A.
      citationCount: 3077
      date: '2019-05-01T00:00:00Z'
      journal: Nature Biotechnology
      title: Assembly of long, error-prone reads using repeat graphs
    note: null
    pmcid: null
    pmid: '30936562'
    type:
    - Primary
    version: null
  - doi: 10.1038/s41592-020-00971-x
    metadata:
      abstract: Long-read sequencing technologies have substantially improved the
        assemblies of many isolate bacterial genomes as compared to fragmented short-read
        assemblies. However, assembling complex metagenomic datasets remains difficult
        even for state-of-the-art long-read assemblers. Here we present metaFlye,
        which addresses important long-read metagenomic assembly challenges, such
        as uneven bacterial composition and intra-species heterogeneity. First, we
        benchmarked metaFlye using simulated and mock bacterial communities and show
        that it consistently produces assemblies with better completeness and contiguity
        than state-of-the-art long-read assemblers. Second, we performed long-read
        sequencing of the sheep microbiome and applied metaFlye to reconstruct 63
        complete or nearly complete bacterial genomes within single contigs. Finally,
        we show that long-read assembly of human microbiomes enables the discovery
        of full-length biosynthetic gene clusters that encode biomedically important
        natural products.
      authors:
      - name: Kolmogorov M.
      - name: Bickhart D.M.
      - name: Behsaz B.
      - name: Gurevich A.
      - name: Rayko M.
      - name: Shin S.B.
      - name: Kuhn K.
      - name: Yuan J.
      - name: Polevikov E.
      - name: Smith T.P.L.
      - name: Pevzner P.A.
      citationCount: 511
      date: '2020-11-01T00:00:00Z'
      journal: Nature Methods
      title: 'metaFlye: scalable long-read metagenome assembly using repeat graphs'
    note: null
    pmcid: PMC10699202
    pmid: '33020656'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 1
  version:
  - 2.9.6
- accessibility: null
  additionDate: '2019-11-14T19:55:10Z'
  biotoolsCURIE: biotools:iNaturalist
  biotoolsID: iNaturalist
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: Methods for broad-scale plant phenology assessments using citizen scientists’
    photographs | iNaturalist.org is a joint initiative of the California Academy
    of Sciences and the National Geographic Society | Explore and share your observations
    from the natural world
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  - doi: 10.1101/754275
    metadata: null
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    pmid: null
    type: []
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  relation: []
  toolType:
  - Database portal
  topic:
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  validated: 1
  version: []
- accessibility: Open access
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  biotoolsCURIE: biotools:barcode_of_life_database
  biotoolsID: barcode_of_life_database
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  description: 'An interactive gateway designed for the tracking and dissemination
    of DNA barcode reference data. The most commonly used marker is a region of the
    cytochrome c oxidase I (COI) gene found in mitochondria but multiple other are
    used for plants and fungi.

    Supported markers:  COI, ITS, rbcL, matK and 18S.'
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    note: null
    operation:
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    - data:
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      format: []
    - data:
        term: Geographic location
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  maturity: Mature
  name: BOLD (Barcode of Life Database)
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  otherID: []
  owner: adriaan
  publication: []
  relation: []
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  - Web API
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Metabarcoding
    uri: http://edamontology.org/topic_4038
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-12-18T00:11:28Z'
  biotoolsCURIE: biotools:pyrx
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    - Primary contact
    url: http://mgl.scripps.edu/
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    name: Alfiya Iksanova
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    orcidid: https://orcid.org/0000-0003-0474-6638
    rorid: null
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    url: null
  description: Virtual Screening software for Computational Drug Discovery that can
    be used to screen libraries of compounds against potential drug targets.
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    type: private
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    operation:
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    metadata:
      abstract: © 2017 The Author(s).Glucokinase is one of the promising targets for
        glucose-lowering agents, and the development of GK activators are now considered
        as one of the most promising strategies for the treatment of type 2 diabetes
        mellitus. In this work, a series of novel symmetric molecular constructs,
        in which two pyridoxine moieties are connected via sulfur-containing linkers,
        have been synthesized and tested in vitro for glucokinase activation potential.
        The enzyme activation rates by two most active compounds at 100 μM (~150%
        and 130%) were comparable to that of the reference agent PF-04937319 (~154%).
        Both leading compounds demonstrated low cytotoxicity and excellent safety
        profile in acute toxicity experiment in rats after oral administration with
        LD50 exceeding 2000 mg/kg of body weight. Binding mode of the active compounds
        in comparison with the reference agent was studied using molecular docking.
        The leading compounds represent viable preclinical candidates for the treatment
        of type 2 diabetes mellitus, as well as a promising starting point for the
        design of structural analogs with improved activity.
      authors:
      - name: Dzyurkevich M.S.
      - name: Babkov D.A.
      - name: Shtyrlin N.V.
      - name: Mayka O.Y.
      - name: Iksanova A.G.
      - name: Vassiliev P.M.
      - name: Balakin K.V.
      - name: Spasov A.A.
      - name: Tarasov V.V.
      - name: Barreto G.
      - name: Shtyrlin Y.G.
      - name: Aliev G.
      citationCount: 7
      date: '2017-12-01T00:00:00Z'
      journal: Scientific Reports
      title: Pyridoxine dipharmacophore derivatives as potent glucokinase activators
        for the treatment of type 2 diabetes mellitus
    note: null
    pmcid: null
    pmid: '29167582'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Drug targets
    uri: http://edamontology.org/topic_0154
  - term: Targets
    uri: http://edamontology.org/topic_0154
  - term: Drug design
    uri: http://edamontology.org/topic_0209
  validated: 1
  version:
  - 0.9.2
next: ?page=2
previous: null
