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@sanger-pathogens

Pathogen Informatics, Wellcome Sanger Institute

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  1. Roary Roary Public

    Rapid large-scale prokaryote pan genome analysis

    Perl 368 192

  2. snp-sites snp-sites Public

    Finds SNP sites from a multi-FASTA alignment file

    C 273 49

  3. Artemis Artemis Public

    Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

    Java 261 77

  4. circlator circlator Public

    A tool to circularize genome assemblies

    Python 252 57

  5. ariba ariba Public

    Antimicrobial Resistance Identification By Assembly

    Python 184 60

  6. assembly-stats assembly-stats Public

    Get assembly statistics from FASTA and FASTQ files

    C++ 124 23

Repositories

Showing 10 of 107 repositories
  • assorted-sub-workflows Public
    sanger-pathogens/assorted-sub-workflows’s past year of commit activity
    Nextflow 0 AGPL-3.0 0 0 0 Updated Feb 6, 2026
  • juno-app Public

    Static site for the Juno project

    sanger-pathogens/juno-app’s past year of commit activity
    JavaScript 0 0 0 5 Updated Feb 4, 2026
  • nextflow-commons Public

    Store of generic templates and scripts for nextflow pipelines

    sanger-pathogens/nextflow-commons’s past year of commit activity
    Nextflow 1 AGPL-3.0 0 0 3 Updated Feb 3, 2026
  • rvi-viral-lens Public
    sanger-pathogens/rvi-viral-lens’s past year of commit activity
    Nextflow 0 0 0 0 Updated Jan 30, 2026
  • rvi-kraken2ref Public
    sanger-pathogens/rvi-kraken2ref’s past year of commit activity
    Python 0 0 0 0 Updated Jan 30, 2026
  • rvi-vl-kraken-prep Public
    sanger-pathogens/rvi-vl-kraken-prep’s past year of commit activity
    Python 0 0 0 0 Updated Jan 27, 2026
  • gps-pipeline-sanger Public Forked from GlobalPneumoSeq/gps-pipeline

    Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)

    sanger-pathogens/gps-pipeline-sanger’s past year of commit activity
    Nextflow 0 GPL-3.0 11 0 1 Updated Jan 26, 2026
  • nextflowtool Public
    sanger-pathogens/nextflowtool’s past year of commit activity
    Groovy 0 AGPL-3.0 0 0 0 Updated Jan 26, 2026
  • assembly_unicycler_short_read Public

    Assembly Unicycler Short Reads

    sanger-pathogens/assembly_unicycler_short_read’s past year of commit activity
    Nextflow 1 MIT 0 0 0 Updated Jan 23, 2026
  • groovy-compare Public

    A Groovy library for comparing two directories, intended to assist in implementing regression-testing for Nextflow pipelines.

    sanger-pathogens/groovy-compare’s past year of commit activity
    Groovy 0 0 0 0 Updated Jan 23, 2026
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