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        The SAMtools and BCFtools packages represent a unique collection of tools
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    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
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  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: '2022-03-22T18:57:49.937151Z'
  biotoolsCURIE: biotools:proteinortho
  biotoolsID: proteinortho
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Marcus Lechner
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sonja J Prohaska
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Proteinortho is a tool to detect orthologous genes within different
    species
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip
    version: null
  - note: Installation with dpkg (root privileges are required)
    type: Downloads page
    url: https://packages.debian.org/unstable/proteinortho
    version: null
  editPermission:
    authors: []
    type: private
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Homology-based gene prediction
      uri: http://edamontology.org/operation_3663
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
  homepage_status: 0
  language:
  - Perl
  - C++
  - Python
  lastUpdate: '2024-03-12T09:10:35.206389Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/paulklemm_PHD/proteinortho
  - note: null
    type:
    - Issue tracker
    url: https://gitlab.com/paulklemm_PHD/proteinortho/-/issues?sort=created_date&state=opened
  - note: null
    type:
    - Galaxy service
    url: https://toolshed.g2.bx.psu.edu/repository?repository_id=584d8accff31aefe&changeset_revision=4850f0d15f01
  maturity: null
  name: Proteinortho
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: klemmp
  publication:
  - doi: 10.1186/1471-2105-12-124
    metadata:
      abstract: 'Background: Orthology analysis is an important part of data analysis
        in many areas of bioinformatics such as comparative genomics and molecular
        phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly
        increasing number of genomes that can be compared simultaneously, calls for
        efficient software tools as brute-force approaches with quadratic memory requirements
        become infeasible in practise. The rapid pace at which new data become available,
        furthermore, makes it desirable to compute genome-wide orthology relations
        for a given dataset rather than relying on relations listed in databases.Results:
        The program Proteinortho described here is a stand-alone tool that is geared
        towards large datasets and makes use of distributed computing techniques when
        run on multi-core hardware. It implements an extended version of the reciprocal
        best alignment heuristic. We apply Proteinortho to compute orthologous proteins
        in the complete set of all 717 eubacterial genomes available at NCBI at the
        beginning of 2009. We identified thirty proteins present in 99% of all bacterial
        proteomes.Conclusions: Proteinortho significantly reduces the required amount
        of memory for orthology analysis compared to existing tools, allowing such
        computations to be performed on off-the-shelf hardware. © 2011 Lechner et
        al; licensee BioMed Central Ltd.'
      authors:
      - name: Lechner M.
      - name: Findeiss S.
      - name: Steiner L.
      - name: Marz M.
      - name: Stadler P.F.
      - name: Prohaska S.J.
      citationCount: 656
      date: '2011-04-28T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'Proteinortho: Detection of (Co-)orthologs in large-scale analysis'
    note: null
    pmcid: PMC3114741
    pmid: '21526987'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 1
  version:
  - 6.0.14
- accessibility: Open access
  additionDate: '2024-03-12T06:13:17.739591Z'
  biotoolsCURIE: biotools:hiv-trace
  biotoolsID: hiv-trace
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: HIV-TRACE is an application that identifies potential transmission
    clusters within a supplied FASTA file.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/veg/hivtrace/archive/refs/tags/0.7.1.zip
    version: 0.1.7
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Operation
      uri: http://edamontology.org/operation_0004
    output:
    - data:
        term: Evidence
        uri: http://edamontology.org/data_2042
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/veg/hivtrace
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2024-03-12T06:13:17.741892Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/veg/hivtrace?tab=readme-ov-file
  maturity: Mature
  name: HIV-TRACE
  operatingSystem: []
  otherID: []
  owner: klemmp
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 0.1.7
- accessibility: Open access
  additionDate: '2024-03-12T00:41:28.027111Z'
  biotoolsCURIE: biotools:getmlst
  biotoolsID: getmlst
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: downloads MLST datasets from pubmlst.org
  documentation: []
  download:
  - note: null
    type: Downloads page
    url: https://github.com/katholt/srst2/archive/refs/tags/v0.2.0.zip
    version: 0.2.0
  editPermission:
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    type: private
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  homepage: https://github.com/katholt/srst2
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2024-03-12T00:41:28.030756Z'
  license: BSD-2-Clause
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/katholt/srst2
  maturity: Mature
  name: GetMLST
  operatingSystem: []
  otherID: []
  owner: klemmp
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 0.2.0
- accessibility: Open access
  additionDate: '2024-03-11T23:56:26.319721Z'
  biotoolsCURIE: biotools:nonpareil
  biotoolsID: nonpareil
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: miguel@rodriguez-r.com
    fundrefid: null
    gridid: null
    name: Luis M Rodriguez-R
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/lmrodriguezr
  description: Estimate metagenomic coverage and sequence diversity
  documentation:
  - note: null
    type:
    - General
    url: https://nonpareil.readthedocs.io
  download:
  - note: null
    type: Source code
    url: https://github.com/lmrodriguezr/nonpareil/archive/refs/tags/v3.4.1.zip
    version: 3.4.1
  editPermission:
    authors: []
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: 'nonpareil -s reads.fa -T kmer -f fastq -b output # fastq is recommended
      for kmer algorithm'
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Operation
      uri: http://edamontology.org/operation_0004
    output:
    - data:
        term: Evidence
        uri: http://edamontology.org/data_2042
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: http://enve-omics.ce.gatech.edu/nonpareil/
  homepage_status: 0
  language: []
  lastUpdate: '2024-03-11T23:56:26.323108Z'
  license: Artistic-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/lmrodriguezr/nonpareil
  maturity: Mature
  name: nonpareil
  operatingSystem: []
  otherID: []
  owner: klemmp
  publication:
  - doi: 10.1093/bioinformatics/btt584
    metadata:
      abstract: 'Motivation: Determining the fraction of the diversity within a microbial
        community sampled and the amount of sequencing required to cover the total
        diversity represent challenging issues for metagenomics studies. Owing to
        these limitations, central ecological questions with respect to the global
        distribution of microbes and the functional diversity of their communities
        cannot be robustly assessed.Results: We introduce Nonpareil, a method to estimate
        and project coverage in metagenomes. Nonpareil does not rely on high-quality
        assemblies, operational taxonomic unit calling or comprehensive reference
        databases; thus, it is broadly applicable to metagenomic studies. Application
        of Nonpareil on available metagenomic datasets provided estimates on the relative
        complexity of soil, freshwater and human microbiome communities, and suggested
        that ∼200 Gb of sequencing data are required for 95% abundance-weighted average
        coverage of the soil communities analyzed. © 2013 The Author 2013. Published
        by Oxford University Press. All rights reserved.'
      authors:
      - name: Rodriguez-R L.M.
      - name: Konstantinidis K.T.
      citationCount: 147
      date: '2014-03-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Nonpareil: A redundancy-based approach to assess the level of coverage
        in metagenomic datasets'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 3.4.1
next: ?page=2
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