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    46 repositories

    • wdl-commons

      Public
      Common WDL task components for bioinformatics workflows.
      WDL
      •
      Other
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • CSP2

      Public
      A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies
      Python
      •
      Other
      •2•4•0•0•Updated Oct 23, 2024Oct 23, 2024

    • CSP2_TestData

      Public
      Repo to store test data for CSP2
      Roff
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • One_Health_Enteric_Package

      Public
      One Health-compatible metadata package for genomic surveillance of enteric microbes
      Creative Commons Attribution 4.0 International
      •2•5•0•0•Updated Oct 4, 2024Oct 4, 2024

    • bettercallsal

      Public
      Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
      nextflowmetagenomicssalmonellanextflow-pipelinesncbi-pathogensquasi-metagenomics
      Nextflow
      •
      Other
      •1•10•0•0•Updated Sep 11, 2024Sep 11, 2024

    • new-porerefiner-plugin

      Public
      Cookiecutter template for a Python package.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1.8k•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • porerefiner

      Public
      A tool for managing your pores
      Python
      •
      Other
      •0•10•1•0•Updated Jul 30, 2024Jul 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.
      nextflowmlstsubtypingnextflow-pipelinescronobacterncbi-pathoges
      Nextflow
      •
      Other
      •1•3•0•0•Updated Jul 16, 2024Jul 16, 2024

    • RIPS

      Public
      RIPS-Rapid Intuitive Pathogen Surveillance
      R
      •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • MultiLab-POD-LOD-ICC

      Public
      This is a Shiny app for interlaboratory microbiological method validation studies.
      R
      •0•1•0•0•Updated May 29, 2024May 29, 2024

    • mlst-hash-template

      Public template
      This is a template for any new hash-based MLST database
      Perl
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • microrunqc-wdl

      Public
      WDL
      •
      Other
      •2•2•0•0•Updated Jan 10, 2024Jan 10, 2024

    • WW-SC2-variant-estimations

      Public
      Other
      •0•2•0•0•Updated Aug 8, 2023Aug 8, 2023

    • C-WAP

      Public
      SC2 variant detection and composition pipeline
      HTML
      •
      Other
      •8•16•3•0•Updated Jul 14, 2023Jul 14, 2023

    • shigatyper

      Public
      CFSAN Shigella Typing Pipeline
      Python
      •
      Other
      •6•14•1•0•Updated Jul 6, 2023Jul 6, 2023

    • vcftoolz

      Public
      Tools for working with Variant Call Format files.
      Python
      •
      Other
      •4•11•7•0•Updated Jun 2, 2023Jun 2, 2023

    • Freyja

      Public
      Depth-weighted De-Mixing
      HTML
      •
      BSD 2-Clause "Simplified" License
      •30•1•0•0•Updated May 22, 2023May 22, 2023

    • 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
      •
      Other
      •31•57•4•1•Updated May 5, 2023May 5, 2023

    • torchbase

      Public
      Python framework for microbial typing by reference
      Python
      •
      Other
      •1•0•0•0•Updated Feb 17, 2023Feb 17, 2023

    • refchooser

      Public
      Tools to help choose a reference from a list of assemblies.
      Python
      •
      Other
      •0•0•1•1•Updated Dec 26, 2022Dec 26, 2022

    • SeroTools

      Public
      A toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping.
      Python
      •
      Other
      •0•2•0•1•Updated Dec 26, 2022Dec 26, 2022

    • kyos

      Public
      Tools for haploid variant calling with Deep Neural Networks.
      Python
      •
      Other
      •0•1•0•1•Updated Dec 26, 2022Dec 26, 2022

    • jobrunner

      Public
      An abstraction layer to run jobs on HPC clusters using Grid Engine, Torque, or locally.
      Python
      •
      Other
      •0•2•0•1•Updated Dec 26, 2022Dec 26, 2022

    • qarrayrun

      Public
      A helper tool for running array jobs on an HPC computational node.
      Python
      •
      Other
      •0•1•0•1•Updated Dec 26, 2022Dec 26, 2022

    • fastatools

      Public
      Tools for working with fasta files.
      Python
      •
      Other
      •0•1•0•1•Updated Dec 26, 2022Dec 26, 2022

    • snp-mutator

      Public
      Generate mutated sequence files from a reference genome.
      Python
      •
      Other
      •4•12•0•1•Updated Dec 26, 2022Dec 26, 2022

    • RabbitTClust

      Public
      RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches
      C++
      •
      Other
      •3•0•0•0•Updated Dec 13, 2022Dec 13, 2022

    • table-ops

      Public
      Python
      •0•0•0•0•Updated Nov 28, 2022Nov 28, 2022

    • ww_simulations

      Public
      Python
      •1•2•1•0•Updated Sep 28, 2022Sep 28, 2022

    • galaxy-worflows

      Public
      Galaxy workflows that are published by CFSAN
      0•0•0•0•Updated Dec 9, 2021Dec 9, 2021