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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 363 191

  2. snp-sites snp-sites Public

    Finds SNP sites from a multi-FASTA alignment file

    C 272 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 260 77

  4. circlator circlator Public

    A tool to circularize genome assemblies

    Python 250 57

  5. ariba ariba Public

    Antimicrobial Resistance Identification By Assembly

    Python 182 59

  6. assembly-stats assembly-stats Public

    Get assembly statistics from FASTA and FASTQ files

    C++ 124 23

Repositories

Showing 10 of 102 repositories
  • BaGPipe Public

    A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge

    sanger-pathogens/BaGPipe’s past year of commit activity
    Nextflow 21 MIT 1 1 3 Updated Jan 8, 2026
  • TpRNAseq Public

    A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data

    sanger-pathogens/TpRNAseq’s past year of commit activity
    Nextflow 2 MIT 1 0 1 Updated Jan 6, 2026
  • 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

    sanger-pathogens/Artemis’s past year of commit activity
    Java 260 77 29 5 Updated Dec 19, 2025
  • juno-app Public

    Static site for the Juno project

    sanger-pathogens/juno-app’s past year of commit activity
    JavaScript 0 0 0 3 Updated Nov 18, 2025
  • BinBaDGer Public
    sanger-pathogens/BinBaDGer’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 6, 2025
  • generate_mags Public
    sanger-pathogens/generate_mags’s past year of commit activity
    Nextflow 2 MIT 0 0 0 Updated Nov 4, 2025
  • Roary Public

    Rapid large-scale prokaryote pan genome analysis

    sanger-pathogens/Roary’s past year of commit activity
    Perl 363 191 192 0 Updated Nov 3, 2025
  • 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 Oct 17, 2025
  • Multiple-mappings-to-bam Public

    A GSoC project - Nextflow pipeline updating the legacy Python2 Multiple mappings to bam to nextflow.

    sanger-pathogens/Multiple-mappings-to-bam’s past year of commit activity
    Python 2 AGPL-3.0 2 1 0 Updated Oct 16, 2025
  • 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 10 0 0 Updated Sep 29, 2025
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