count: 3379
list:
- accessibility: Open access
  additionDate: '2015-08-24T08:35:55Z'
  biotoolsCURIE: biotools:bcftools
  biotoolsID: bcftools
  collectionID:
  - BCFtools
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: BCFtools is a set of utilities that manipulate variant calls in the
    Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently
    with both VCFs and BCFs, both uncompressed and BGZF-compressed.
  documentation:
  - note: null
    type:
    - General
    url: http://www.htslib.org/doc/bcftools.html
  - note: A workflow for BCFtools.
    type:
    - Other
    url: http://www.htslib.org/workflow/#mapping_to_variant
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: Multiple data munging operations.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-04-16T10:25:06.228249Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/bcftools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/bcftools/issues
  maturity: Mature
  name: BCFtools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata:
      abstract: 'Summary: The Sequence Alignment/Map (SAM) format is a generic alignment
        format for storing read alignments against reference sequences, supporting
        short and long reads (up to 128 Mbp) produced by different sequencing platforms.
        It is flexible in style, compact in size, efficient in random access and is
        the format in which alignments from the 1000 Genomes Project are released.
        SAM tools implements various utilities for post-processing alignments in the
        SAM format, such as indexing, variant caller and alignment viewer, and thus
        provides universal tools for processing read alignments. © 2009 The Author(s).'
      authors:
      - name: Li H.
      - name: Handsaker B.
      - name: Wysoker A.
      - name: Fennell T.
      - name: Ruan J.
      - name: Homer N.
      - name: Marth G.
      - name: Abecasis G.
      - name: Durbin R.
      citationCount: 37126
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: 'Background: SAMtools and BCFtools are widely used programs for processing
        and analysing high-throughput sequencing data. They include tools for file
        format conversion and manipulation, sorting, querying, statistics, variant
        calling, and effect analysis amongst other methods. Findings: The first version
        appeared online 12 years ago and has been maintained and further developed
        ever since, with many new features and improvements added over the years.
        The SAMtools and BCFtools packages represent a unique collection of tools
        that have been used in numerous other software projects and countless genomic
        pipelines. Conclusion: Both SAMtools and BCFtools are freely available on
        GitHub under the permissive MIT licence, free for both non-commercial and
        commercial use. Both packages have been installed >1 million times via Bioconda.
        The source code and documentation are available from https://www.htslib.org.'
      authors:
      - name: Danecek P.
      - name: Bonfield J.K.
      - name: Liddle J.
      - name: Marshall J.
      - name: Ohan V.
      - name: Pollard M.O.
      - name: Whitwham A.
      - name: Keane T.
      - name: McCarthy S.A.
      - name: Davies R.M.
      citationCount: 3084
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Command-line tool
  - Suite
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
- accessibility: Open access
  additionDate: '2017-01-13T13:16:12Z'
  biotoolsCURIE: biotools:samtools
  biotoolsID: samtools
  collectionID:
  - Rare Disease
  - Animal and Crop Genomics
  - SAMtools
  community:
    biolib:
      app_name: samtools
      author_name: SAMtools
      author_username: samtools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: rd@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Richard Durbin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: SAMtools and BCFtools are widely used programs for processing and analysing
    high-throughput sequencing data. They include tools for file format conversion
    and manipulation, sorting, querying, statistics, variant calling, and effect analysis
    amongst other methods.
  documentation:
  - note: HowTos for samtools
    type:
    - Other
    url: http://www.htslib.org/doc/#howtos
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  - note: null
    type:
    - Installation instructions
    url: http://www.htslib.org/download/
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - ELIXIR-EE
    - animalandcropgenomics
    - alice
    - awhitwham
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
    note: null
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Editing
      uri: http://edamontology.org/operation_3096
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    - term: Sorting
      uri: http://edamontology.org/operation_3802
    - term: Filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-04-16T10:22:46.809965Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/samtools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/samtools/issues
  maturity: Mature
  name: SAMtools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata:
      abstract: 'Summary: The Sequence Alignment/Map (SAM) format is a generic alignment
        format for storing read alignments against reference sequences, supporting
        short and long reads (up to 128 Mbp) produced by different sequencing platforms.
        It is flexible in style, compact in size, efficient in random access and is
        the format in which alignments from the 1000 Genomes Project are released.
        SAM tools implements various utilities for post-processing alignments in the
        SAM format, such as indexing, variant caller and alignment viewer, and thus
        provides universal tools for processing read alignments. © 2009 The Author(s).'
      authors:
      - name: Li H.
      - name: Handsaker B.
      - name: Wysoker A.
      - name: Fennell T.
      - name: Ruan J.
      - name: Homer N.
      - name: Marth G.
      - name: Abecasis G.
      - name: Durbin R.
      citationCount: 37126
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: 'Background: SAMtools and BCFtools are widely used programs for processing
        and analysing high-throughput sequencing data. They include tools for file
        format conversion and manipulation, sorting, querying, statistics, variant
        calling, and effect analysis amongst other methods. Findings: The first version
        appeared online 12 years ago and has been maintained and further developed
        ever since, with many new features and improvements added over the years.
        The SAMtools and BCFtools packages represent a unique collection of tools
        that have been used in numerous other software projects and countless genomic
        pipelines. Conclusion: Both SAMtools and BCFtools are freely available on
        GitHub under the permissive MIT licence, free for both non-commercial and
        commercial use. Both packages have been installed >1 million times via Bioconda.
        The source code and documentation are available from https://www.htslib.org.'
      authors:
      - name: Danecek P.
      - name: Bonfield J.K.
      - name: Liddle J.
      - name: Marshall J.
      - name: Ohan V.
      - name: Pollard M.O.
      - name: Whitwham A.
      - name: Keane T.
      - name: McCarthy S.A.
      - name: Davies R.M.
      citationCount: 3084
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btr509
    metadata:
      abstract: 'Motivation: Most existing methods for DNA sequence analysis rely
        on accurate sequences or genotypes. However, in applications of the next-generation
        sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample
        low-coverage sequencing or somatic mutation discovery). These applications
        press for the development of new methods for analyzing sequence data with
        uncertainty. Results: We present a statistical framework for calling SNPs,
        discovering somatic mutations, inferring population genetical parameters and
        performing association tests directly based on sequencing data without explicit
        genotyping or linkage-based imputation. On real data, we demonstrate that
        our method achieves comparable accuracy to alternative methods for estimating
        site allele count, for inferring allele frequency spectrum and for association
        mapping. We also highlight the necessity of using symmetric datasets for finding
        somatic mutations and confirm that for discovering rare events, mismapping
        is frequently the leading source of errors. © The Author 2011. Published by
        Oxford University Press. All rights reserved.'
      authors:
      - name: Li H.
      citationCount: 3826
      date: '2011-11-01T00:00:00Z'
      journal: Bioinformatics
      title: A statistical framework for SNP calling, mutation discovery, association
        mapping and population genetical parameter estimation from sequencing data
    note: null
    pmcid: PMC3198575
    pmid: '21903627'
    type: []
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Suite
  - Command-line tool
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
  - Animal and Crop Genomics
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - animalandcropgenomics
    - smoe
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-04-16T10:19:42.968075Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/htslib
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/htslib/issues
  maturity: Mature
  name: HTSlib
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/gigascience/giab007
    metadata:
      abstract: 'Background: Since the original publication of the VCF and SAM formats,
        an explosion of software tools have been created to process these data files.
        To facilitate this a library was produced out of the original SAMtools implementation,
        with a focus on performance and robustness. The file formats themselves have
        become international standards under the jurisdiction of the Global Alliance
        for Genomics and Health. Findings: We present a software library for providing
        programmatic access to sequencing alignment and variant formats. It was born
        out of the widely used SAMtools and BCFtools applications. Considerable improvements
        have been made to the original code plus many new features including newer
        access protocols, the addition of the CRAM file format, better indexing and
        iterators, and better use of threading. Conclusion: Since the original Samtools
        release, performance has been considerably improved, with a BAM read-write
        loop running 5 times faster and BAM to SAM conversion 13 times faster (both
        using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen
        HTSlib downloaded >1 million times from GitHub and conda. The C library has
        been used directly by an estimated 900 GitHub projects and has been incorporated
        into Perl, Python, Rust, and R, significantly expanding the number of uses
        via other languages. HTSlib is open source and is freely available from htslib.org
        under MIT/BSD license.'
      authors:
      - name: Bonfield J.K.
      - name: Marshall J.
      - name: Danecek P.
      - name: Li H.
      - name: Ohan V.
      - name: Whitwham A.
      - name: Keane T.
      citationCount: 116
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: 'HTSlib: C library for reading/writing high-Throughput sequencing data'
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
    pmcid: PMC7931820
    pmid: '33594436'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: samtools
    type: usedBy
  - biotoolsID: bcftools
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - 1.2.1
  - '1.3'
  - 1.3.1
  - 1.3.2
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
- accessibility: Open access
  additionDate: '2024-03-12T14:45:13.869292Z'
  biotoolsCURIE: biotools:vegan
  biotoolsID: vegan
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Ordination methods, diversity analysis and other functions for community
    and vegetation ecologists
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Analysis
      uri: http://edamontology.org/operation_2945
    output: []
  homepage: https://cran.r-project.org/web/packages/vegan/index.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-03-12T14:45:13.871787Z'
  license: GPL-2.0
  link: []
  maturity: Mature
  name: vegan
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Environmental science
    uri: http://edamontology.org/topic_3855
  validated: 0
  version:
  - 2.4-3
  - 2.6-4
- accessibility: Open access
  additionDate: '2024-03-12T14:25:30.909146Z'
  biotoolsCURIE: biotools:usher
  biotoolsID: usher
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: The UShER toolkit includes a set of tools for for rapid, accurate placement
    of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic
    analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing
    in that its placement is orders of magnitude faster and more memory-efficient
    than previous methods.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Phylogenetic inference (from molecular sequences)
      uri: http://edamontology.org/operation_0540
    output: []
  homepage: https://github.com/yatisht/usher
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2024-03-12T14:36:05.717126Z'
  license: MIT
  link: []
  maturity: Mature
  name: usher
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Cladistics
    uri: http://edamontology.org/topic_3944
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  validated: 0
  version:
  - 0.2.1
- accessibility: Open access
  additionDate: '2024-03-12T14:08:55.216456Z'
  biotoolsCURIE: biotools:sonneityping
  biotoolsID: sonneityping
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Scripts for parsing Mykrobe predict results for Shigella sonnei.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Antimicrobial resistance prediction
      uri: http://edamontology.org/operation_3482
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output: []
  homepage: https://github.com/katholt/sonneityping
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-03-12T14:08:55.221529Z'
  license: MIT
  link: []
  maturity: Mature
  name: sonneityping
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - '20210201'
- accessibility: Open access
  additionDate: '2024-03-12T13:53:58.513919Z'
  biotoolsCURIE: biotools:qiime_core
  biotoolsID: qiime_core
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: QIIME 2™ is a next-generation microbiome bioinformatics platform that
    is extensible, free, open source, and community developed.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Demultiplexing
      uri: http://edamontology.org/operation_3933
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Phylogenetic analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output: []
  homepage: http://qiime.org/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-03-12T13:53:58.516554Z'
  license: BSD-3-Clause
  link: []
  maturity: Mature
  name: qiime_core
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Metatranscriptomics
    uri: http://edamontology.org/topic_3941
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-03-12T13:42:43.483763Z'
  biotoolsCURIE: biotools:qiime_add_on
  biotoolsID: qiime_add_on
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: QIIME 2 is a next-generation microbiome bioinformatics platform that
    is extensible, free, open source, and community developed.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Demultiplexing
      uri: http://edamontology.org/operation_3933
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Phylogenetic analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output: []
  homepage: http://qiime.org/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-03-12T13:42:43.486440Z'
  license: BSD-3-Clause
  link: []
  maturity: Mature
  name: qiime_add_on
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Metatranscriptomics
    uri: http://edamontology.org/topic_3941
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-03-12T13:15:07.749827Z'
  biotoolsCURIE: biotools:mykrobe-parser
  biotoolsID: mykrobe-parser
  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  credit: []
  description: RScript to parse the results of mykrobe predictor.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Analysis
      uri: http://edamontology.org/operation_2945
    - term: Antimicrobial resistance prediction
      uri: http://edamontology.org/operation_3482
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output: []
  homepage: https://github.com/phac-nml/mykrobe-parser
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-03-12T13:18:08.517327Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: mykrobe-parser
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  topic:
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - 0.1.4.1
- accessibility: Open access
  additionDate: '2024-03-12T10:56:44.977314Z'
  biotoolsCURIE: biotools:lorikeet
  biotoolsID: lorikeet
  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  credit: []
  description: Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output: []
  homepage: https://github.com/AbeelLab/lorikeet
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2024-03-12T10:56:44.980036Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: lorikeet
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version:
  - '20'
next: ?page=2
previous: null
