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  1. snp-pipeline snp-pipeline Public

    SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

    Python 59 33

  2. C-WAP C-WAP Public

    SC2 variant detection and composition pipeline

    HTML 17 8

  3. shigatyper shigatyper Public

    CFSAN Shigella Typing Pipeline

    Python 14 7

  4. snp-mutator snp-mutator Public

    Generate mutated sequence files from a reference genome.

    Python 12 5

  5. vcftoolz vcftoolz Public

    Tools for working with Variant Call Format files.

    Python 12 5

  6. bettercallsal bettercallsal Public

    Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

    Nextflow 11 2

Repositories

Showing 10 of 50 repositories
  • nowayout Public

    nowayout is a super-fast automated software pipeline for taxonomic classification of Eukaryotic mitochondrial reads.

    Nextflow 1 0 0 0 Updated Jul 24, 2025
  • CSP2 Public

    A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies

    Python 6 5 1 0 Updated Jun 25, 2025
  • bettercallsal Public

    Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

    Nextflow 11 2 0 0 Updated Jun 24, 2025
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    Shell 0 MIT 3,560 0 0 Updated Jun 20, 2025
  • centriflaken Public

    centriflaken

    Nextflow 1 0 0 0 Updated Jun 17, 2025
  • wdl-commons Public

    Common WDL task components for bioinformatics workflows.

    WDL 0 1 0 0 Updated Jun 11, 2025
  • data-commons Public
    0 0 0 0 Updated Jun 6, 2025
  • One_Health_Enteric_Package Public

    One Health-compatible metadata package for genomic surveillance of enteric microbes

    6 CC-BY-4.0 3 1 0 Updated Apr 15, 2025
  • Seqsero2_galaxy Public

    Galaxy wrapper for denglab's SeqSero2

    Makefile 0 0 0 0 Updated Mar 26, 2025
  • MultiLab-POD-LOD-ICC Public

    This is a Shiny app for interlaboratory microbiological method validation studies.

    R 1 1 0 0 Updated Feb 21, 2025