Pinned Repositories
bettercallsal
Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
C-WAP
SC2 variant detection and composition pipeline
CSP2
A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies
One_Health_Enteric_Package
One Health-compatible metadata package for genomic surveillance of enteric microbes
porerefiner
A tool for managing your pores
SeroTools
A toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping.
shigatyper
CFSAN Shigella Typing Pipeline
snp-mutator
Generate mutated sequence files from a reference genome.
snp-pipeline
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.
vcftoolz
Tools for working with Variant Call Format files.
CFSAN (Center for Food Safety and Applied Nutrition)'s Repositories
CFSAN-Biostatistics/snp-pipeline
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.
CFSAN-Biostatistics/C-WAP
SC2 variant detection and composition pipeline
CFSAN-Biostatistics/shigatyper
CFSAN Shigella Typing Pipeline
CFSAN-Biostatistics/snp-mutator
Generate mutated sequence files from a reference genome.
CFSAN-Biostatistics/porerefiner
A tool for managing your pores
CFSAN-Biostatistics/vcftoolz
Tools for working with Variant Call Format files.
CFSAN-Biostatistics/bettercallsal
Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
CFSAN-Biostatistics/One_Health_Enteric_Package
One Health-compatible metadata package for genomic surveillance of enteric microbes
CFSAN-Biostatistics/CSP2
A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies
CFSAN-Biostatistics/cronology
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/jobrunner
An abstraction layer to run jobs on HPC clusters using Grid Engine, Torque, or locally.
CFSAN-Biostatistics/microrunqc-wdl
CFSAN-Biostatistics/SeroTools
A toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping.
CFSAN-Biostatistics/WW-SC2-variant-estimations
CFSAN-Biostatistics/ww_simulations
CFSAN-Biostatistics/fastatools
Tools for working with fasta files.
CFSAN-Biostatistics/Freyja
Depth-weighted De-Mixing
CFSAN-Biostatistics/kyos
Tools for haploid variant calling with Deep Neural Networks.
CFSAN-Biostatistics/MultiLab-POD-LOD-ICC
This is a Shiny app for interlaboratory microbiological method validation studies.
CFSAN-Biostatistics/qarrayrun
A helper tool for running array jobs on an HPC computational node.
CFSAN-Biostatistics/amrfinder-galaxy
amrfinder-galaxy
CFSAN-Biostatistics/alphafold2
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
CFSAN-Biostatistics/galaxy-worflows
Galaxy workflows that are published by CFSAN
CFSAN-Biostatistics/mlst-hash-template
This is a template for any new hash-based MLST database
CFSAN-Biostatistics/RabbitTClust
RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches
CFSAN-Biostatistics/refchooser
Tools to help choose a reference from a list of assemblies.
CFSAN-Biostatistics/RIPS
RIPS-Rapid Intuitive Pathogen Surveillance
CFSAN-Biostatistics/table-ops
CFSAN-Biostatistics/torchbase
Python framework for microbial typing by reference
CFSAN-Biostatistics/wdl-commons
Common WDL task components for bioinformatics workflows.