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  description: "Free, browser-based tool to open almost any sequence file — FASTA,\
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  name: picklet
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  owner: fishka
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  toolType:
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  - Desktop application
  topic:
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    uri: http://edamontology.org/topic_0091
  - term: Nucleic acids
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  validated: 0
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- accessibility: Open access
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  biotoolsID: ab1lens
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  cost: Free of charge
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  name: ab1lens
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  owner: fishka
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  toolType:
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  - term: Data visualisation
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  - term: Whole genome sequencing
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  validated: 0
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  biotoolsID: linkset-automation
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: linkset-automation is a set of tools to automatically generates CyTargetLinker
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  documentation:
  - note: null
    type:
    - Command-line options
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  - note: null
    type: Source code
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      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Data deposition
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    - term: Statistical calculation
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    - data:
        term: Data reference
        uri: http://edamontology.org/data_2093
      format:
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  language:
  - Shell
  - Python
  lastUpdate: '2026-07-10T08:57:45.592347Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/CyTargetLinker/linkset-automation
  maturity: Emerging
  name: linkset-automation
  operatingSystem: []
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  owner: n.m.palmblad@lumc.nl
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  - doi: 10.12688/f1000research.14613.2
    metadata: null
    note: null
    pmcid: PMC6707396
    pmid: '31489175'
    type:
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    version: null
  - doi: 10.1186/s13059-019-1758-4
    metadata: null
    note: General description of automation in Cytoscape
    pmcid: PMC6717989
    pmid: '31477170'
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    version: null
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    type: uses
  - biotoolsID: cytoscape
    type: uses
  - biotoolsID: bridgedb
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Biochemistry
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  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-06-18T10:26:39.717312Z'
  biotoolsCURIE: biotools:pico_galaxy
  biotoolsID: pico_galaxy
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Short Python script (using Biopython library functions) to extract
    sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
    by a column of a tabular file. The output order follows that of the tabular file,
    and if there are duplicates in the tabular file, there will be duplicates in the
    output sequence file.
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    input:
    - data:
        term: Sequence
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      format:
      - term: qual
        uri: http://edamontology.org/format_3607
      - term: SFF
        uri: http://edamontology.org/format_3284
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: SFF
        uri: http://edamontology.org/format_3284
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
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  homepage_status: 0
  language:
  - Shell
  - Python
  lastUpdate: '2026-07-10T08:17:07.983990Z'
  license: Not licensed
  link: []
  maturity: Mature
  name: pico_galaxy
  operatingSystem: []
  otherID: []
  owner: walter3
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version:
  - v0.0.15
- accessibility: Open access
  additionDate: '2026-07-10T05:37:33.802700Z'
  biotoolsCURIE: biotools:figtracer
  biotoolsID: figtracer
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: David Priest
    note: null
    orcidid: https://orcid.org/0000-0003-0095-6718
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: null
  description: Plain-text, git-tracked electronic lab notebook (ELN) for reproducible
    bioinformatics — threads your R & Python figures into living lab notes with full
    provenance. Built for single-cell / CyTOF / flow cytometry; works with Obsidian,
    Quarto & Jupyter.
  documentation: []
  download: []
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  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-10T05:44:46.759713Z'
  license: MIT
  link: []
  maturity: Emerging
  name: figtracer
  operatingSystem: []
  otherID: []
  owner: david6
  publication:
  - doi: 10.5281/zenodo.21288980
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Library
  - Command-line tool
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Cytometry
    uri: http://edamontology.org/topic_3934
  - term: Data management
    uri: http://edamontology.org/topic_3071
  - term: Software engineering
    uri: http://edamontology.org/topic_3372
  validated: 0
  version:
  - 0.1.0
- accessibility: null
  additionDate: '2023-10-31T13:37:59.723864Z'
  biotoolsCURIE: biotools:kraken2tax
  biotoolsID: kraken2tax
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: This tool converts data from Kraken to a Galaxy taxonomy representation.
  documentation: []
  download: []
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    authors: []
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  function:
  - cmd: null
    input: []
    note: null
    operation:
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  homepage: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax
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  language: []
  lastUpdate: '2026-07-10T02:41:46.235321Z'
  license: null
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  name: Kraken2Tax
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  owner: admin
  publication:
  - doi: 10.1186/gb-2014-15-3-r46
    metadata:
      abstract: Kraken is an ultrafast and highly accurate program for assigning taxonomic
        labels to metagenomic DNA sequences. Previous programs designed for this task
        have been relatively slow and computationally expensive, forcing researchers
        to use faster abundance estimation programs, which only classify small subsets
        of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification
        accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken
        classifies 100 base pair reads at a rate of over 4.1 million reads per minute,
        909 times faster than Megablast and 11 times faster than the abundance estimation
        program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.
        © 2014 Wood and Salzberg; licensee BioMed Central Ltd.
      authors:
      - name: Wood D.E.
      - name: Salzberg S.L.
      citationCount: 2889
      date: '2014-03-03T00:00:00Z'
      journal: Genome Biology
      title: 'Kraken: Ultrafast metagenomic sequence classification using exact alignments'
    note: null
    pmcid: PMC4053813
    pmid: '24580807'
    type: []
    version: null
  - doi: 10.1101/gr.094508.109
    metadata:
      abstract: How many species inhabit our immediate surroundings? A straightforward
        collection technique suitable for answering this question is known to anyone
        who has ever driven a car at highway speeds. The windshield of a moving vehicle
        is subjected to numerous insect strikes and can be used as a collection device
        for representative sampling. Unfortunately the analysis of biological material
        collected in that manner, as with most metagenomic studies, proves to be rather
        demanding due to the large number of required tools and considerable computational
        infrastructure. In this study, we use organic matter collected by a moving
        vehicle to design and test a comprehensive pipeline for phylogenetic profiling
        of metagenomic samples that includes all steps from processing and quality
        control of data generated by next-generation sequencing technologies to statistical
        analyses and data visualization. To the best of our knowledge, this is also
        the first publication that features a live online supplement providing access
        to exact analyses and workflows used in the article. © 2009 by Cold Spring
        Harbor Laboratory Press.
      authors:
      - name: Pond S.K.
      - name: Wadhawan S.
      - name: Chiaromonte F.
      - name: Ananda G.
      - name: Chung W.-Y.
      - name: Taylor J.
      - name: Nekrutenko A.
      citationCount: 59
      date: '2009-11-01T00:00:00Z'
      journal: Genome Research
      title: Windshield splatter analysis with the Galaxy metagenomic pipeline
    note: null
    pmcid: PMC2775585
    pmid: '19819906'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: null
  additionDate: '2022-02-24T00:12:40.833213Z'
  biotoolsCURIE: biotools:mothur
  biotoolsID: mothur
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Open-source, platform-independent, community-supported software for
    describing and comparing microbial communities
  documentation:
  - note: null
    type:
    - User manual
    url: http://mothur.org/wiki/mothur_manual/
  - note: mothur Wiki page
    type:
    - Other
    url: http://mothur.org/wiki/
  download: []
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    authors: []
    type: public
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: DNA barcoding
      uri: http://edamontology.org/operation_3200
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence read processing
      uri: http://edamontology.org/operation_3921
    - term: Phylogenetic analysis
      uri: http://edamontology.org/operation_0324
    output: []
  homepage: http://mothur.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-07-10T02:41:43.627271Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mothur/mothur
  - note: mothur GitHub organization
    type:
    - Other
    - Repository
    url: https://github.com/mothur
  maturity: null
  name: mothur
  operatingSystem: []
  otherID: []
  owner: admin
  publication:
  - doi: 10.1128/aem.01541-09
    metadata:
      abstract: Mothur aims to be a comprehensive software package that allows users
        to use a single piece of software to analyze community sequence data. It builds
        upon previous tools to provide a flexible and powerful software package for
        analyzing sequencing data. As a case study, we used mothur to trim, screen,
        and align sequences; calculate distances; assign sequences to operational
        taxonomic units; and describe the α and β diversity of eight marine samples
        previously characterized by pyrosequencing of 16S rRNA gene fragments. This
        analysis of more than 222,000 sequences was completed in less than 2 h with
        a laptop computer. Copyright © 2009, American Society for Microbiology. All
        Rights Reserved.
      authors:
      - name: Schloss P.D.
      - name: Westcott S.L.
      - name: Ryabin T.
      - name: Hall J.R.
      - name: Hartmann M.
      - name: Hollister E.B.
      - name: Lesniewski R.A.
      - name: Oakley B.B.
      - name: Parks D.H.
      - name: Robinson C.J.
      - name: Sahl J.W.
      - name: Stres B.
      - name: Thallinger G.G.
      - name: Van Horn D.J.
      - name: Weber C.F.
      citationCount: 16666
      date: '2009-12-01T00:00:00Z'
      journal: Applied and Environmental Microbiology
      title: 'Introducing mothur: Open-source, platform-independent, community-supported
        software for describing and comparing microbial communities'
    note: null
    pmcid: PMC2786419
    pmid: '19801464'
    type: []
    version: null
  relation: []
  toolType:
  - Suite
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-02-23T01:01:27.707985Z'
  biotoolsCURIE: biotools:anndata
  biotoolsID: anndata
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'From https://anndata.readthedocs.io/en/latest/

    "Python package for handling annotated data matrices in memory and on disk, positioned
    between pandas and xarray."'
  documentation:
  - note: null
    type:
    - General
    url: https://anndata.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: public
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  homepage: https://github.com/scverse/anndata
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-10T02:41:41.032876Z'
  license: BSD-3-Clause
  link: []
  maturity: null
  name: anndata
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  owner: admin
  publication:
  - doi: 10.1101/2021.12.16.473007
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2023-11-03T03:32:25.637178Z'
  biotoolsCURIE: biotools:t2t_report
  biotoolsID: t2t_report
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Given taxonomy representation (produced by *Taxonomy manipulation->Fetch
    Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks."
    - Galaxy tool wrapper
  documentation:
  - note: null
    type:
    - User manual
    url: https://docs.rs/taxonomy/latest/taxonomy/json/enum.JsonFormat.html
  download: []
  editPermission:
    authors: []
    type: public
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Read summarisation
      uri: http://edamontology.org/operation_3793
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output: []
  homepage: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report
  homepage_status: 0
  language: []
  lastUpdate: '2026-07-10T02:41:26.642020Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/onecodex/taxonomy/
  maturity: null
  name: Summarize taxonomy
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: null
  additionDate: '2023-11-03T03:26:35.915870Z'
  biotoolsCURIE: biotools:t2ps
  biotoolsID: t2ps
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: '"Given taxonomy representation (produced by *Fetch taxonomic representation*
    tool) this utility produces a graphical representations of phylogenetic tree in
    PDF format." - Galaxy tool wrapper'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/galaxyproject/tools-devteam/blob/9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml#L51
  download: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    output: []
  homepage: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps
  homepage_status: 0
  language: []
  lastUpdate: '2026-07-10T02:41:24.077065Z'
  license: null
  link: []
  maturity: null
  name: Draw phylogeny
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  validated: 0
  version: []
- accessibility: null
  additionDate: '2023-11-03T03:50:29.356720Z'
  biotoolsCURIE: biotools:format_metaphlan2_output
  biotoolsID: format_metaphlan2_output
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: This tool format output file of MetaPhlan2 containing community content
    (abundance) at all taxonomic levels (from kingdom to strains).
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output: []
  homepage: https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output
  homepage_status: 0
  language: []
  lastUpdate: '2026-07-10T02:41:21.751369Z'
  license: null
  link: []
  maturity: null
  name: Format metaphlan2 output
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: null
  additionDate: '2023-11-03T03:45:00.826990Z'
  biotoolsCURIE: biotools:compare_humann2_outputs
  biotoolsID: compare_humann2_outputs
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: This tool compare HUMANnN2 outputs with gene families or pathways and
    their relative abundances between several samples
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    output: []
  homepage: https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
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