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HFP (Human Foods Program)

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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 57 31

  2. C-WAP C-WAP Public

    SC2 variant detection and composition pipeline

    HTML 16 8

  3. shigatyper shigatyper Public

    CFSAN Shigella Typing Pipeline

    Python 14 6

  4. snp-mutator snp-mutator Public

    Generate mutated sequence files from a reference genome.

    Python 12 4

  5. vcftoolz vcftoolz Public

    Tools for working with Variant Call Format files.

    Python 11 4

  6. porerefiner porerefiner Public

    A tool for managing your pores

    Python 10

Repositories

Showing 10 of 46 repositories
  • wdl-commons Public

    Common WDL task components for bioinformatics workflows.

    CFSAN-Biostatistics/wdl-commons’s past year of commit activity
    WDL 0 0 0 0 Updated Nov 6, 2024
  • CSP2 Public

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

    CFSAN-Biostatistics/CSP2’s past year of commit activity
    Python 4 2 0 0 Updated Oct 23, 2024
  • CSP2_TestData Public

    Repo to store test data for CSP2

    CFSAN-Biostatistics/CSP2_TestData’s past year of commit activity
    Roff 0 GPL-3.0 0 0 0 Updated Oct 17, 2024
  • One_Health_Enteric_Package Public

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

    CFSAN-Biostatistics/One_Health_Enteric_Package’s past year of commit activity
    5 CC-BY-4.0 2 0 0 Updated Oct 4, 2024
  • bettercallsal Public

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

    CFSAN-Biostatistics/bettercallsal’s past year of commit activity
    Nextflow 10 1 0 0 Updated Sep 11, 2024
  • new-porerefiner-plugin Public Forked from audreyfeldroy/cookiecutter-pypackage

    Cookiecutter template for a Python package.

    CFSAN-Biostatistics/new-porerefiner-plugin’s past year of commit activity
    Python 0 BSD-3-Clause 1,837 0 0 Updated Jul 31, 2024
  • porerefiner Public

    A tool for managing your pores

    CFSAN-Biostatistics/porerefiner’s past year of commit activity
    Python 10 0 1 0 Updated Jul 30, 2024
  • cronology Public

    cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.

    CFSAN-Biostatistics/cronology’s past year of commit activity
    Nextflow 3 1 0 0 Updated Jul 16, 2024
  • RIPS Public

    RIPS-Rapid Intuitive Pathogen Surveillance

    CFSAN-Biostatistics/RIPS’s past year of commit activity
    R 0 0 0 0 Updated Jun 10, 2024
  • MultiLab-POD-LOD-ICC Public

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

    CFSAN-Biostatistics/MultiLab-POD-LOD-ICC’s past year of commit activity
    R 1 0 0 0 Updated May 29, 2024
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