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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 342 190

  2. snp-sites snp-sites Public

    Finds SNP sites from a multi-FASTA alignment file

    C 257 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 245 76

  4. circlator circlator Public

    A tool to circularize genome assemblies

    Python 240 57

  5. ariba ariba Public

    Antimicrobial Resistance Identification By Assembly

    Python 174 55

  6. assembly-stats assembly-stats Public

    Get assembly statistics from FASTA and FASTQ files

    C++ 119 21

Repositories

Showing 10 of 93 repositories
  • ONTAP Public

    Nextflow pipeline for accurate pathogen typing from ONT amplicon sequencing data

    sanger-pathogens/ONTAP’s past year of commit activity
    Nextflow 2 AGPL-3.0 0 0 0 Updated Apr 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 1 0 0 Updated Apr 16, 2025
  • assorted-sub-workflows Public
    sanger-pathogens/assorted-sub-workflows’s past year of commit activity
    Nextflow 0 AGPL-3.0 0 0 0 Updated Apr 9, 2025
  • 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 12 MIT 1 0 0 Updated Mar 25, 2025
  • Fastaq Public

    Python3 scripts to manipulate FASTA and FASTQ files

    sanger-pathogens/Fastaq’s past year of commit activity
    Python 70 21 8 2 Updated Mar 24, 2025
  • pymummer Public

    Python3 module for running MUMmer and reading the output

    sanger-pathogens/pymummer’s past year of commit activity
    Python 32 10 4 0 Updated Mar 24, 2025
  • gps-pipeline 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’s past year of commit activity
    Nextflow 0 GPL-3.0 10 0 2 Updated Feb 5, 2025
  • nextflowtool Public
    sanger-pathogens/nextflowtool’s past year of commit activity
    Groovy 0 AGPL-3.0 0 0 0 Updated Jan 31, 2025
  • Unicycler Public Forked from rrwick/Unicycler

    hybrid assembly pipeline for bacterial genomes

    sanger-pathogens/Unicycler’s past year of commit activity
    C++ 1 GPL-3.0 137 0 0 Updated Dec 19, 2024
  • bactgen-training-app Public

    Static site for training on the Juno/GPS2 projects

    sanger-pathogens/bactgen-training-app’s past year of commit activity
    HTML 0 1 0 0 Updated Dec 12, 2024
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