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/alphafold2
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
CFSAN-Biostatistics/ncbi-pathogen-api-docs
Repository for samizdat about NCBI's undocumented Pathogen API.
CFSAN-Biostatistics/vauxite
Vauxite - an in-silico sequence typing framework
CFSAN-Biostatistics/LexMapr-Galaxy
LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
CFSAN-Biostatistics/SeqSero2-galaxy
SeqSero2
CFSAN-Biostatistics/snps_in_genes
A tool for finding what genes SNPs detected with the CFSAN SNP Pipeline reside in
CFSAN-Biostatistics/wgs_competency
Templates for quantitative and graphical reports summarizing bacterial whole genome DNA sequencing competency assessment analyses.
CFSAN-Biostatistics/kmer_id
Identification of WGS reads by kmer database
CFSAN-Biostatistics/amr_curation
A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.
CFSAN-Biostatistics/usegalaxy-eu-tools
List of tools included in https://usegalaxy.eu
CFSAN-Biostatistics/ephemeris
Library for managing Galaxy plugins - tools, index data, and workflows.
CFSAN-Biostatistics/sra-tools
SRA Tools
CFSAN-Biostatistics/miso-lims
MISO: An open-source LIMS for NGS sequencing centres
CFSAN-Biostatistics/tools-devteam
Contains a set of Galaxy Tools mostly written by the Galaxy Team.
CFSAN-Biostatistics/spades
SPAdes Genome Assembler http://cab.spbu.ru/spades