count: 2071
list:
- accessibility: null
  additionDate: '2023-06-07T03:22:25.847061Z'
  biotoolsCURIE: biotools:metabuli
  biotoolsID: metabuli
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Metabuli: specific and sensitive metagenomic classification via joint
    analysis of DNA and amino acid'
  documentation: []
  download: []
  editPermission:
    authors:
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  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: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format: []
  homepage: https://metabuli.steineggerlab.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-12T14:21:25.897853Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/steineggerlab/Metabuli/issues
  - note: github repository
    type:
    - Repository
    url: https://github.com/steineggerlab/Metabuli
  maturity: Mature
  name: metabuli
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/s41592-024-02273-y
    metadata: null
    note: null
    pmcid: null
    pmid: '38769467'
    type: []
    version: null
  relation:
  - biotoolsID: mmseqs2
    type: uses
  - biotoolsID: gtdb
    type: uses
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: null
  additionDate: '2019-06-20T14:18:28Z'
  biotoolsCURIE: biotools:decompTumor2Sig
  biotoolsID: decompTumor2Sig
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: r.piro@fu-berlin.de
    fundrefid: null
    gridid: null
    name: Prof. Dr. Rosario M. Piro
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: R package for identification of mutational signatures active in individual
    tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type
    or Shiraishi-type signatures, thus quantifying the contribution of the corresponding
    mutational processes to the somatic mutations identified in the tumor.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf
  download:
  - note: null
    type: Downloads page
    url: http://rmpiro.net/index.html#downloads
    version: null
  editPermission:
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    - ELIXIR-ITA-POLIMI
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: http://rmpiro.net/decompTumor2Sig/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-02T08:12:42.981321Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/rmpiro/decompTumor2Sig/issues
  - note: null
    type:
    - Repository
    url: https://github.com/rmpiro/decompTumor2Sig
  - note: null
    type:
    - Software catalogue
    url: https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html
  maturity: Mature
  name: decompTumor2Sig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1186/s12859-019-2688-6
    metadata:
      abstract: '© 2019 The Author(s).Background: The somatic mutations found in a
        tumor have in most cases been caused by multiple mutational processes such
        as those related to extrinsic carcinogens like cigarette smoke, and those
        related to intrinsic processes like age-related spontaneous deamination of
        5-methylcytosine. The effect of such mutational processes can be modeled by
        mutational signatures, of which two different conceptualizations exist: the
        model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model
        introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial
        identification and definition of mutational signatures requires large sets
        of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use
        R package that can decompose an individual tumor genome into a given set of
        Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution
        of the corresponding mutational processes to the somatic mutations identified
        in the tumor. Until now, such tools were available only for Alexandrov signatures.
        We demonstrate the correctness and usefulness of our approach with three test
        cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor
        genomes of ten different tumor entities, and from simulated tumor genomes,
        respectively. Conclusions: The decompTumor2Sig package is freely available
        and has been accepted for inclusion in Bioconductor.'
      authors:
      - name: Kruger S.
      - name: Piro R.M.
      citationCount: 8
      date: '2019-04-18T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'DecompTumor2Sig: Identification of mutational signatures active in individual
        tumors'
    note: null
    pmcid: PMC6472187
    pmid: '30999866'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2026-01-30T22:36:14.902508Z'
  biotoolsCURIE: biotools:pantas
  biotoolsID: pantas
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Differential quantification of alternative splicing events on spliced
    pangenome graphs.
  documentation:
  - note: null
    type:
    - General
    - Installation instructions
    - Quick start guide
    - Command-line options
    url: https://github.com/AlgoLab/pantas/blob/main/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/AlgoLab/pantas
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/algolab/pantas
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/algolab/pantas
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-30T22:36:14.904749Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AlgoLab/pantas
  - note: null
    type:
    - Issue tracker
    url: https://github.com/AlgoLab/pantas/issues
  maturity: null
  name: pantas
  operatingSystem:
  - Linux
  otherID: []
  owner: yp
  publication:
  - doi: 10.1371/journal.pcbi.1012665
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: RNA splicing
    uri: http://edamontology.org/topic_3320
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-27T17:11:15.880698Z'
  biotoolsCURIE: biotools:recgraph
  biotoolsID: recgraph
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: RecGraph is a tool for computing optimal sequence-to-graph alignment
    with recombinations.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/AlgoLab/RecGraph/blob/main/README.md
  download:
  - note: null
    type: Binaries
    url: https://github.com/AlgoLab/RecGraph/releases/tag/v1.0.0
    version: 1.0.0
  - note: null
    type: Software package
    url: https://anaconda.org/channels/bioconda/packages/recgraph/overview
    version: null
  editPermission:
    authors: []
    type: group
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/AlgoLab/RecGraph
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2026-01-30T22:07:27.044664Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AlgoLab/RecGraph
  - note: null
    type:
    - Issue tracker
    url: https://github.com/AlgoLab/RecGraph/issues
  maturity: Emerging
  name: RecGraph
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: yp
  publication:
  - doi: 10.1093/bioinformatics/btae292
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 1.0.0
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Population genomics
    uri: http://edamontology.org/topic_3796
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2021-05-08T17:25:21Z'
  biotoolsCURIE: biotools:bakta
  biotoolsID: bakta
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: oliver.schwengers@cb.jlug.de
    fundrefid: null
    gridid: null
    name: Oliver Schwengers
    note: null
    orcidid: https://orcid.org/0000-0003-4216-2721
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/oschwengers
  - email: null
    fundrefid: null
    gridid: null
    name: Justus Liebig University Giessen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-giessen.de
  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/oschwengers/bakta/blob/main/README.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md
  - note: null
    type:
    - Code of conduct
    url: https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md
  - note: null
    type:
    - User manual
    url: https://bakta.readthedocs.io/
  download:
  - note: Mandatory annotation database
    type: Other
    url: https://zenodo.org/records/14916843
    version: v6.0
  editPermission:
    authors:
    - ELIXIR-CZ
    - bebatut
    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format:
      - term: HMMER3
        uri: http://edamontology.org/format_3329
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-29T12:11:19.042627Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/oschwengers/bakta
  - note: null
    type:
    - Issue tracker
    url: https://github.com/oschwengers/bakta/issues
  - note: null
    type:
    - Other
    url: https://bioconda.github.io/recipes/bakta/README.html
  - note: null
    type:
    - Service
    url: https://bakta.computational.bio
  maturity: Mature
  name: Bakta
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata: null
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  - doi: 10.1093/nar/gkaf335
    metadata: null
    note: null
    pmcid: PMC12230652
    pmid: '40271661'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: diamond
    type: uses
  - biotoolsID: hmmer3
    type: uses
  - biotoolsID: infernal
    type: uses
  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: aragorn
    type: uses
  - biotoolsID: pilercr
    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - v1.12.0
- accessibility: null
  additionDate: '2021-09-27T07:31:29.303373Z'
  biotoolsCURIE: biotools:icodon
  biotoolsID: icodon
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: arb@stowers.org
    fundrefid: null
    gridid: null
    name: Ariel Alejandro Bazzini
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: iCodon is a tool for ideal codon design for customized gene expression.
  documentation: []
  download: []
  editPermission:
    authors:
    - jian
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Nucleic acid design
      uri: http://edamontology.org/operation_3095
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: cis-regulatory element prediction
      uri: http://edamontology.org/operation_0441
    output: []
  homepage: https://bazzinilab.shinyapps.io/icodon/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-28T15:28:03.870976Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/santiago1234/iCodon
  - note: null
    type:
    - Issue tracker
    url: https://github.com/santiago1234/iCodon/issues
  maturity: null
  name: iCodon
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1101/2021.05.06.442969
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Library
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Biotechnology
    uri: http://edamontology.org/topic_3297
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version: []
- 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://github.com/DerrickWood/kraken2
  homepage_status: 0
  language:
  - Perl
  - C++
  lastUpdate: '2026-01-28T10:34:30.102754Z'
  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
  - biotoolsID: gtdb
    type: uses
  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: Open access
  additionDate: '2026-01-26T15:47:19.914992Z'
  biotoolsCURIE: biotools:dome_registry
  biotoolsID: dome_registry
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: gavinmichael.farrell@phd.unipd.it
    fundrefid: null
    gridid: null
    name: Gavin Farrell
    note: Curation and data support
    orcidid: https://orcid.org/0000-0001-5166-8551
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
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      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
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      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-11T14:16:30.074724Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
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  - note: Twitter feed
    type:
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    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/104771886/
  maturity: Mature
  name: Jalview
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  otherID: []
  owner: ben_s
  publication:
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    metadata:
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      authors: []
      citationCount: 7717
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.5.1
- accessibility: null
  additionDate: '2024-12-21T15:24:55.662209Z'
  biotoolsCURIE: biotools:stripepy
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  description: StripePy recognizes architectural stripes in 3C and Hi-C contact maps
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  - note: null
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  toolType:
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  topic:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-12-09T09:22:22.735091Z'
  biotoolsCURIE: biotools:instanovo
  biotoolsID: instanovo
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: k.eloff@instadeep.com
    fundrefid: null
    gridid: null
    name: Kevin Eloff
    note: null
    orcidid: https://orcid.org/0000-0003-1355-8743
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: konka@dtu.dk
    fundrefid: null
    gridid: null
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    note: null
    orcidid: https://orcid.org/0000-0003-3907-9281
    rorid: null
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    typeRole:
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    url: null
  - email: r.catzel@instadeep.com
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    note: null
    orcidid: https://orcid.org/0000-0002-2983-9833
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: j.vangoey@instadeep.com
    fundrefid: null
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    name: Jeroen Van Goey
    note: null
    orcidid: https://orcid.org/0000-0003-4480-5567
    rorid: null
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    typeRole:
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    url: null
  - email: tpaje@dtu.dk
    fundrefid: null
    gridid: null
    name: Timothy P. Jenkins
    note: null
    orcidid: https://orcid.org/0000-0003-2979-5663
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  description: InstaNovo is a transformer neural network with the ability to translate
    fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).
  documentation:
  - note: null
    type:
    - General
    url: https://instadeepai.github.io/InstaNovo/
  - note: null
    type:
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    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/#installation
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    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/
  - note: null
    type:
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    url: https://instadeepai.github.io/InstaNovo/reference/cli/
  - note: null
    type:
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    url: https://instadeepai.github.io/InstaNovo/API/summary/
  - note: null
    type:
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    url: https://instadeepai.github.io/InstaNovo/citation/
  download:
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  editPermission:
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  function:
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        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    output:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/instadeepai/instanovo
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-09T21:41:17.117080Z'
  license: Apache-2.0
  link:
  - note: null
    type:
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    url: https://github.com/instadeepai/instanovo
  - note: null
    type:
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  - note: null
    type:
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  - note: null
    type:
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  maturity: Mature
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  otherID: []
  owner: BioGeek
  publication:
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    metadata:
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      authors: []
      citationCount: 7
      date: '2025-04-01T00:00:00Z'
      journal: Nature Machine Intelligence
      title: InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale
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    note: null
    pmcid: null
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  topic:
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  - term: Proteins
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  - term: Proteomics experiment
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  - term: Machine learning
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  validated: 0
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- accessibility: null
  additionDate: '2024-04-18T08:31:46.459964Z'
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  description: 'Python bindings for hictk: read and write .cool and .hic files directly
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  documentation:
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    note: null
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  toolType:
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  - term: Sequence analysis
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  validated: 0
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  additionDate: '2017-08-03T18:45:53Z'
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  description: "HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis\
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    \ continue to be available via SourceForge. \n\nHBAT 2.0 was introduced in 2025\
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    version: 2.x
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      format:
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        uri: http://edamontology.org/format_1476
    note: null
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      format: []
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  language:
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  lastUpdate: '2025-11-29T17:30:01.186940Z'
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    type:
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  owner: abhishektiwari
  publication:
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    metadata: null
    note: Peer-reviewed paper for HBAT 1.0
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  topic:
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  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2025-11-28T17:29:53.564906Z'
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    url: https://www.recetox.muni.cz/en/services/data-services-2/spectrometric-data-processing-and-analysis
  description: 'This package performs in-silico MeOX + TMS derivatization (as described
    e.g. in https://doi.org/10.1021/acs.analchem.7b01010):


    Methoximation: ketone R(C=O)R'' and aldehyde (-HC=O) carbonyl groups are substituted
    with -C=NOCH3

    Trimethylsilylation: the acidic hydrogen in -OH, -SH, -COOH, -NH2, -NHR, =NH,
    the hydrogen is substituted with -Si(CH3)3 The substitution doesn''t always have
    to happen; its probability is currently hardcoded in the package. Typically, multiple
    substitution attempts are run on each input molecule, and all distinct results
    are gathered.

    Known limitation is methoximation on cycles which should be broken. This is not
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    - Command-line options
    url: https://github.com/RECETOX/gc-meox-tms/blob/master/README.md
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    - Training material
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  function:
  - cmd: add_derivatization_groups()
    input:
    - data:
        term: SMILES string
        uri: http://edamontology.org/data_2301
      format: []
    note: Produces MeOX/TMS derivatives of given compounds
    operation:
    - term: Sequence editing
      uri: http://edamontology.org/operation_0231
    output:
    - data:
        term: SMILES string
        uri: http://edamontology.org/data_2301
      format: []
  homepage: https://github.com/RECETOX/gc-meox-tms
  homepage_status: 0
  language:
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  lastUpdate: '2025-11-28T17:42:43.031944Z'
  license: MIT
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      citationCount: 2439
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  - doi: 10.1101/079681
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  - doi: 10.1093/bioinformatics/bty1057
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    version: null
  - doi: 10.1101/2024.11.13.623350v1
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  credit: []
  description: Folddisco enables rapid detection of discontinuous or segment 3D motifs
    in large protein databses.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/steineggerlab/folddisco
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2025-11-10T08:25:02.388051Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/steineggerlab/folddisco/issues
  - note: null
    type:
    - Service
    url: https://search.foldseek.com/folddisco
  maturity: Emerging
  name: Folddisco
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1101/2025.07.06.663357v1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Protein structural motifs and surfaces
    uri: http://edamontology.org/topic_0166
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-02-28T15:04:33.594183Z'
  biotoolsCURIE: biotools:prolfquapp
  biotoolsID: prolfquapp
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line tool for differential expression analysis in quantitative
    proteomics
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/prolfqua/prolfquapp/blob/master/README.md
  download:
  - note: null
    type: Downloads page
    url: https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6
    version: 0.1.6
  editPermission:
    authors:
    - thatmariia
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: './prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis
      -s DIANN

      # and again you run the version within the docker container with

      # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y
      config.yaml -w NameOfAnalysis -s DIANN'
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-06T14:37:12.116175Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/prolfqua/prolfquapp
  - note: null
    type:
    - Issue tracker
    url: https://github.com/prolfqua/prolfquapp/issues
  maturity: Emerging
  name: prolfquapp
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.4c00911
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2025-02-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential
        Expression Analysis in Quantitative Proteomics
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.0.6
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 0.1.6
- accessibility: Open access
  additionDate: '2019-08-09T13:14:25Z'
  biotoolsCURIE: biotools:El-MAVEN
  biotoolsID: El-MAVEN
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: info@elucidata.io
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: elmaven@elucidata.io
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine
    for Metabolomics.
  documentation:
  - note: null
    type:
    - User manual
    url: https://elucidatainc.github.io/ElMaven/documentation/
  download:
  - note: null
    type: Binaries
    url: https://elucidatainc.github.io/ElMaven/Downloads/
    version: null
  - note: null
    type: Source code
    url: https://github.com/ElucidataInc/ElMaven/releases
    version: null
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/ElucidataInc/ElMaven
  homepage_status: 0
  language: []
  lastUpdate: '2025-11-03T16:47:19.388844Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ElucidataInc/ElMaven
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ElucidataInc/ElMaven/issues
  maturity: Mature
  name: El-MAVEN
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hans
  publication:
  - doi: 10.1007/978-1-4939-9236-2_19
    metadata:
      abstract: ''
      authors: []
      citationCount: 106
      date: '2019-01-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: 'EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing
        engine for metabolomics'
    note: null
    pmcid: null
    pmid: '31119671'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-07-04T14:05:39Z'
  biotoolsCURIE: biotools:CliqueMS
  biotoolsID: CliqueMS
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: oriol.senan@urv.cat
    fundrefid: null
    gridid: null
    name: Oriol Senan
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Computational tool for annotating in-source metabolite ions from LC-MS
    untargeted metabolomics data based on a coelution similarity network.
  documentation:
  - note: Tutorial material
    type:
    - Training material
    url: https://github.com/osenan/cliqueMS/blob/master/vignettes/annotate_features.Rmd
  download:
  - note: null
    type: Source code
    url: https://cran.r-project.org/src/contrib/Archive/cliqueMS/
    version: null
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Read binning
      uri: http://edamontology.org/operation_3798
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    output: []
  homepage: https://github.com/osenan/cliqueMS
  homepage_status: 0
  language:
  - R
  - C++
  lastUpdate: '2025-11-03T16:44:03.166147Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/osenan/cliqueMS/issues
  maturity: Mature
  name: CliqueMS
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1093/bioinformatics/btz207
    metadata:
      abstract: 'The analysis of biological samples in untargeted metabolomic studies
        using LC-MS yields tens of thousands of ion signals. Annotating these features
        is of the utmost importance for answering questions as fundamental as, e.g.
        how many metabolites are there in a given sample.Results: Here, we introduce
        CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is
        based on the similarity between coelution profiles and therefore, as opposed
        to most methods, allows for the annotation of a single spectrum. Furthermore,
        CliqueMS improves upon the state of the art in several dimensions: (i) it
        uses a more discriminatory feature similarity metric; (ii) it treats the similarities
        between features in a transparent way by means of a simple generativemodel;
        (iii) it uses a well-grounded maximum likelihood inference approach to group
        features; (iv) it uses empirical adduct frequencies to identify the parental
        mass and (v) it deals more flexibly with the identification of the parental
        mass by proposing and ranking alternative annotations. We validate our approach
        with simple mixtures of standards and with real complex biological samples.
        CliqueMS reduces the thousands of features typically obtained in complex samples
        to hundreds of metabolites, and it is able to correctly annotate more metabolites
        and adducts from a single spectrum than available tools.'
      authors:
      - name: Senan O.
      - name: Aguilar-Mogas A.
      - name: Navarro M.
      - name: Capellades J.
      - name: Noon L.
      - name: Burks D.
      - name: Yanes O.
      - name: Guimera R.
      - name: Sales-Pardo M.
      citationCount: 48
      date: '2019-10-15T00:00:00Z'
      journal: Bioinformatics
      title: 'CliqueMS: A computational tool for annotating in-source metabolite ions
        from LC-MS untargeted metabolomics data based on a coelution similarity network'
    note: null
    pmcid: PMC6792096
    pmid: '30903689'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version:
  - 0.3.2
- accessibility: Open access
  additionDate: '2019-08-26T14:34:55Z'
  biotoolsCURIE: biotools:MINERVA_Platform
  biotoolsID: MINERVA_Platform
  collectionID:
  - LCSB
  - ELIXIR-LU
  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: '2025-10-29T08:54:40.647322Z'
  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: ''
      authors: []
      citationCount: 71
      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: ''
      authors: []
      citationCount: 26
      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: ''
      authors: []
      citationCount: 18
      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: ''
      authors: []
      citationCount: 40
      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: ''
      authors: []
      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
  - 19.1.0
- accessibility: Open access
  additionDate: '2024-03-07T20:51:08.529472Z'
  biotoolsCURIE: biotools:oncoanalyser
  biotoolsID: oncoanalyser
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Oncoanalyser is an nf-core Nextflow implementation of the tools developed
    by Hartwig Medical Foundation. The workflow is designed to comprehensively detect
    all variant types (SNV. MNV, InDel, SV, CNV, Fusions, Viral insertions, Telomere
    length, Genetic Immune Escape, mutational processes) as well as key tumor characteristics
    (purity, ploidy, TMB, MSI) from data derived from different short read platforms.
    The tooling is optimised for paired whole genome samples (90x tumor, 30x normal)
    but can be run on exome or panel (targeted) data. There is support for GRCh37
    and GRCh38 human reference genome builds.
  documentation: []
  download: []
  editPermission:
    authors:
    - jdeligt
    - VKasalica
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/nf-core/oncoanalyser/tree/dev
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-10-09T07:39:49.943872Z'
  license: GPL-3.0
  link:
  - note: GitHub page for issue tracking of Nextflow workflow implementation
    type:
    - Issue tracker
    - Repository
    url: https://github.com/nf-core/oncoanalyser/tree/dev
  - note: GitHub repository of underlying tools with issue tracking
    type:
    - Repository
    - Issue tracker
    url: https://github.com/hartwigmedical/hmftools
  maturity: Mature
  name: oncoanalyser
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: jdeligt
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - '5.34'
- accessibility: null
  additionDate: '2021-11-01T10:50:55.880296Z'
  biotoolsCURIE: biotools:pastaq
  biotoolsID: pastaq
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: p.l.horvatovich@rug.nl
    fundrefid: null
    gridid: null
    name: Peter Horvatovich
    note: null
    orcidid: https://orcid.org/0000-0003-2218-1140
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: PASTAQ (Pipelines And Systems for Threshold Avoiding Quantification)
    provides a set of tools for high-performance pre-processing of LC-MS/MS data.
    Avoiding the use of arbitrary intensity thresholds in early stages of the pipeline
    can aid in the detection of important biological low intensity signals common
    in metabolomics and proteomics experiments.
  documentation: []
  download: []
  editPermission:
    authors:
    - n.m.palmblad@lumc.nl
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    output: []
  homepage: https://pastaq.horvatovichlab.com
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2025-10-01T14:14:12.464961Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/PASTAQ-MS/PASTAQ
  - note: null
    type:
    - Issue tracker
    url: https://github.com/PASTAQ-MS/PASTAQ/issues
  maturity: null
  name: PASTAQ
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1021/acs.analchem.1c01892
    metadata:
      abstract: ''
      authors: []
      citationCount: 10
      date: '2021-08-17T00:00:00Z'
      journal: Analytical Chemistry
      title: Pipelines and Systems for Threshold-Avoiding Quantification of LC-MS/MS
        Data
    note: null
    pmcid: PMC8374884
    pmid: '34355890'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Workflow
  - Library
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteomics
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  - term: Metabolomics
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  - term: Workflows
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  - term: Small molecules
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  validated: 0
  version: []
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    rorid: null
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  description: 'BEACON is a computational framework designed to perform Bayesian analysis
    on expression and gene dependency data across different cell lineages. The model
    integrates expression as the dependent variable and gene dependency data as the
    independent variable.


    The framework uses JAGS (Just Another Gibbs Sampler) for Bayesian inference and
    MCMC (Markov Chain Monte Carlo) simulations to estimate parameters of interest,
    including the correlation between gene expression and dependency.'
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  license: MIT
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  owner: aelmas
  publication:
  - doi: 10.1101/2024.10.17.618926
    metadata: null
    note: null
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    pmid: '39484404'
    type:
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  topic:
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  - term: Gene regulation
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-09-17T13:10:30.804502Z'
  biotoolsCURIE: biotools:gffx
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    url: https://github.com/Baohua-Chen
  description: GFFx is a Rust-based toolkit for ultra-fast and scalable genome annotation
    access. GFFx introduces a compact, model-aware indexing system inspired by binning
    strategies and leverages Rust’s strengths in execution speed, memory safety, and
    multithreading. It supports feature- and region-based feature extraction and coverage
    profiling with significant improvements in runtime and scalability over existing
    tools.
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      format:
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  - cmd: gffx depth -i input.gff -s source.bam -o output.txt
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    - data:
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      format:
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    note: null
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      format:
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  homepage_status: 0
  language:
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  lastUpdate: '2025-09-17T13:27:25.403064Z'
  license: Apache-2.0
  link:
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    metadata: null
    note: null
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  toolType:
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  topic:
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  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
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  additionDate: '2025-09-10T13:36:20.945616Z'
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  description: Ultrafast preprocessing and quality control for long reads (Nanopore,
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  license: MIT
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  publication:
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    pmcid: PMC10989850
    pmid: '38868435'
    type:
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  topic:
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  validated: 0
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- accessibility: Open access
  additionDate: '2025-08-20T09:24:38.732312Z'
  biotoolsCURIE: biotools:omicflow
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  description: A generalised data structure for fast and efficient loading and data
    munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata
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    by aligning them into a single object that is defined as an 'omics' class. Once
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  - note: null
    type:
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  license: MIT
  link:
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  toolType:
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  topic:
  - term: Metagenomics
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  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 1.3.0
- accessibility: Open access
  additionDate: '2025-07-23T10:24:09.622930Z'
  biotoolsCURIE: biotools:xnatpy
  biotoolsID: xnatpy
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
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  description: Python package to interact with the XNAT REST API in a python data-science
    way
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  topic:
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  - term: FAIR data
    uri: http://edamontology.org/topic_4012
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  additionDate: '2025-07-10T12:32:00.838316Z'
  biotoolsCURIE: biotools:inmoose
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    url: https://www.epigenelabs.com/
  description: InMoose, the INtegrated Multi-Omic Open-Source environment, ports to
    Python state-of-the-art R tools for the analysis of transcriptomic data.
  documentation:
  - note: null
    type:
    - General
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  - note: null
    type:
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      uri: http://edamontology.org/operation_3223
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  language:
  - Python
  lastUpdate: '2025-07-10T13:00:37.310588Z'
  license: GPL-3.0
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  publication:
  - doi: 10.1038/s41598-025-03376-y
    metadata:
      abstract: We introduce InMoose, an open-source Python environment aimed at omic
        data analysis. We illustrate its capabilities for bulk transcriptomic data
        analysis. Due to its wide adoption, Python has grown as a de facto standard
        in fields increasingly important for bioinformatic pipelines, such as data
        science, machine learning, or artificial intelligence (AI). As a general-purpose
        language, Python is also recognized for its versatility and scalability. InMoose
        aims at bringing state-of-the-art tools, historically written in R, to the
        Python ecosystem. InMoose focuses on providing drop-in replacements for R
        tools, to ensure consistency and reproducibility between R-based and Python-based
        pipelines. The first development phase has focused on bulk transcriptomic
        data, with current capabilities encompassing data simulation, batch effect
        correction, and differential analysis and meta-analysis.
      authors:
      - name: Colange M.
      - name: Appe G.
      - name: Meunier L.
      - name: Weill S.
      - name: Johnson W.E.
      - name: Nordor A.
      - name: Behdenna A.
      citationCount: 1
      date: '2025-12-01T00:00:00Z'
      journal: Scientific Reports
      title: Bridging the gap between R and Python in bulk transcriptomic data analysis
        with InMoose
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    - Usage
    version: null
  - doi: 10.1186/s12859-023-05578-5
    metadata:
      abstract: 'Background: Variability in datasets is not only the product of biological
        processes: they are also the product of technical biases. ComBat and ComBat-Seq
        are among the most widely used tools for correcting those technical biases,
        called batch effects, in, respectively, microarray and RNA-Seq expression
        data. Results: In this technical note, we present a new Python implementation
        of ComBat and ComBat-Seq. While the mathematical framework is strictly the
        same, we show here that our implementations: (i) have similar results in terms
        of batch effects correction; (ii) are as fast or faster than the original
        implementations in R and; (iii) offer new tools for the bioinformatics community
        to participate in its development. pyComBat is implemented in the Python language
        and is distributed under GPL-3.0 (https://www.gnu.org/licenses/gpl-3.0.en.html)
        license as a module of the inmoose package. Source code is available at https://github.com/epigenelabs/inmoose
        and Python package at https://pypi.org/project/inmoose . Conclusions: We present
        a new Python implementation of state-of-the-art tools ComBat and ComBat-Seq
        for the correction of batch effects in microarray and RNA-Seq data. This new
        implementation, based on the same mathematical frameworks as ComBat and ComBat-Seq,
        offers similar power for batch effect correction, at reduced computational
        cost.'
      authors:
      - name: Behdenna A.
      - name: Colange M.
      - name: Haziza J.
      - name: Gema A.
      - name: Appe G.
      - name: Azencott C.-A.
      - name: Nordor A.
      citationCount: 30
      date: '2023-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: pyComBat, a Python tool for batch effects correction in high-throughput
        molecular data using empirical Bayes methods
    note: null
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    - Method
    version: null
  - doi: 10.1186/s12859-025-06180-7
    metadata:
      abstract: 'Background: Differential gene expression analysis is a prominent
        technique for the analysis of biomolecular data to identify genetic features
        associated with phenotypes. Limma—for microarray data –, and edgeR and DESeq2—for
        RNA-Seq data–, are the most widely used tools for differential gene expression
        analysis of bulk transcriptomic data. Results: We present the differential
        expression features of InMoose, a Python implementation of R tools limma,
        edgeR, and DESeq2. We experimentally show that InMoose stands as a drop-in
        replacement for those tools, with nearly identical results. This ensures reproducibility
        when interfacing both languages in bioinformatic pipelines. InMoose is an
        open source software released under the GPL3 license, available at www.github.com/epigenelabs/inmoose
        and https://inmoose.readthedocs.io. Conclusions: We present a new Python implementation
        of state-of-the-art tools limma, edgeR, and DESeq2, to perform differential
        gene expression analysis of bulk transcriptomic data. This new implementation
        exhibits results nearly identical to the original tools, improving interoperability
        and reproducibility between Python and R bioinformatics pipelines.'
      authors:
      - name: Colange M.
      - name: Appe G.
      - name: Meunier L.
      - name: Weill S.
      - name: Nordor A.
      - name: Behdenna A.
      citationCount: 0
      date: '2025-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: Differential expression analysis with inmoose, the integrated multi-omic
        open-source environment in Python
    note: null
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    - Method
    version: null
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  topic: []
  validated: 0
  version:
  - 0.8.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-07-10T03:21:50.923918Z'
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  cost: Free of charge (with restrictions)
  credit: []
  description: The dataset consists of 572 slices (specimens) with 20,592 images.
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    training (train+val) set and testing set are provided in the Zenodo repository.
    Source code in Github is to train and validate five deep learning models using
    ColoPola dataset.
  documentation: []
  download:
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    version: '1.0'
  - note: Dataset for running source code
    type: Test data
    url: https://zenodo.org/records/10554304
    version: '1.2'
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function: []
  homepage: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-10T03:33:52.616431Z'
  license: CC0-1.0
  link:
  - note: Source code
    type:
    - Repository
    url: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset
  - note: null
    type:
    - Issue tracker
    url: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset/issues
  maturity: Mature
  name: ColoPola dataset for colorectal cancer detection
  operatingSystem:
  - Windows
  otherID: []
  owner: haile
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2017-01-17T15:07:47Z'
  biotoolsCURIE: biotools:copasi
  biotoolsID: copasi
  collectionID:
  - de.NBI
  - EBI Training Tools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://copasi.org/About/Team/
  - email: frank.bergmann@bioquant.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Frank T. Bergmann
    note: null
    orcidid: https://orcid.org/0000-0001-5553-4702
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Open-source software application for creating and solving mathematical
    models of biological processes such as metabolic networks, cell-signaling pathways,
    regulatory networks, infectious diseases, and many others. It includes features
    to define models of biological processes, simulate and analyze these models, generate
    analysis reports, and import/export models in SBML format.
  documentation:
  - note: null
    type:
    - User manual
    url: http://copasi.org/Support/User_Manual/
  download:
  - note: Source and binary packages are available for download.
    type: Binaries
    url: http://copasi.org/Download/
    version: null
  editPermission:
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    type: private
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  elixirNode:
  - Germany
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
    note: null
    operation:
    - term: Network simulation
      uri: http://edamontology.org/operation_3562
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Metabolic network modelling
      uri: http://edamontology.org/operation_3660
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
  homepage: http://copasi.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-07-07T11:17:37.638447Z'
  license: Artistic-2.0
  link:
  - note: User Forum
    type:
    - Discussion forum
    url: https://groups.google.com/g/copasi-user-forum
  - note: Issue tracker
    type:
    - Issue tracker
    url: http://tracker.copasi.org/
  - note: Github Repo
    type:
    - Repository
    url: https://github.com/copasi/COPASI
  - note: null
    type:
    - Social media
    url: https://fosstodon.org/@copasi
  maturity: Mature
  name: COPASI
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: frankbergmann
  publication:
  - doi: 10.1093/bioinformatics/btl485
    metadata:
      abstract: 'Motivation: Simulation and modeling is becoming a standard approach
        to understand complex biochemical processes. Therefore, there is a big need
        for software tools that allow access to diverse simulation and modeling methods
        as well as support for the usage of these methods. Results: Here, we present
        COPASI, a platform-independent and user-friendly biochemical simulator that
        offers several unique features. We discuss numerical issues with these features;
        in particular, the criteria to switch between stochastic and deterministic
        simulation methods, hybrid deterministic-stochastic methods, and the importance
        of random number generator numerical resolution in stochastic simulation.
        © 2006 Oxford University Press.'
      authors:
      - name: Hoops S.
      - name: Gauges R.
      - name: Lee C.
      - name: Pahle J.
      - name: Simus N.
      - name: Singhal M.
      - name: Xu L.
      - name: Mendes P.
      - name: Kummer U.
      citationCount: 2004
      date: '2006-12-15T00:00:00Z'
      journal: Bioinformatics
      title: COPASI - A COmplex PAthway SImulator
    note: null
    pmcid: null
    pmid: '17032683'
    type: []
    version: null
  - doi: 10.1007/978-1-59745-525-1_2
    metadata:
      abstract: Computational modeling and simulation of biochemical networks is at
        the core of systems biology and this includes many types of analyses that
        can aid understanding of how these systems work. COPASI is a generic software
        package for modeling and simulation of biochemical networks which provides
        many of these analyses in convenient ways that do not require the user to
        program or to have deep knowledge of the numerical algorithms. Here we provide
        a description of how these modeling techniques can be applied to biochemical
        models using COPASI. The focus is both on practical aspects of software usage
        as well as on the utility of these analyses in aiding biological understanding.
        Practical examples are described for steady-state and time-course simulations,
        stoichiometric analyses, parameter scanning, sensitivity analysis (including
        metabolic control analysis), global optimization, parameter estimation, and
        stochastic simulation. The examples used are all published models that are
        available in the BioModels database in SBML format. © 2009 Humana Press.
      authors:
      - name: Mendes P.
      - name: Hoops S.
      - name: Sahle S.
      - name: Gauges R.
      - name: Dada J.
      - name: Kummer U.
      citationCount: 171
      date: '2009-12-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: Computational modeling of biochemical networks using COPASI
    note: null
    pmcid: null
    pmid: '19399433'
    type: []
    version: null
  - doi: 10.1016/j.jbiotec.2017.06.1200
    metadata:
      abstract: COPASI is software used for the creation, modification, simulation
        and computational analysis of kinetic models in various fields. It is open-source,
        available for all major platforms and provides a user-friendly graphical user
        interface, but is also controllable via the command line and scripting languages.
        These are likely reasons for its wide acceptance. We begin this review with
        a short introduction describing the general approaches and techniques used
        in computational modeling in the biosciences. Next we introduce the COPASI
        package, and its capabilities, before looking at typical applications of COPASI
        in biotechnology.
      authors:
      - name: Bergmann F.T.
      - name: Hoops S.
      - name: Klahn B.
      - name: Kummer U.
      - name: Mendes P.
      - name: Pahle J.
      - name: Sahle S.
      citationCount: 81
      date: '2017-11-10T00:00:00Z'
      journal: Journal of Biotechnology
      title: COPASI and its applications in biotechnology
    note: null
    pmcid: PMC5623632
    pmid: '28655634'
    type: []
    version: null
  relation:
  - biotoolsID: corc
    type: usedBy
  - biotoolsID: pycotools
    type: usedBy
  - biotoolsID: biosimulations
    type: includedIn
  - biotoolsID: sbmlwebapp
    type: usedBy
  - biotoolsID: libsbml
    type: uses
  toolType:
  - Command-line tool
  - Library
  - Desktop application
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 1
  version: []
- 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
  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
    - 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
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  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: 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: '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:
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    - 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
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