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CFSAN (Center for Food Safety and Applied Nutrition)'s Projects

alphafold2 icon alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

amr_curation icon amr_curation

A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.

bettercallsal icon bettercallsal

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

c-wap icon c-wap

SC2 variant detection and composition pipeline

cronology icon cronology

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

csp2 icon csp2

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

ephemeris icon ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.

jobrunner icon jobrunner

An abstraction layer to run jobs on HPC clusters using Grid Engine, Torque, or locally.

kmer_id icon kmer_id

Identification of WGS reads by kmer database

kyos icon kyos

Tools for haploid variant calling with Deep Neural Networks.

lexmapr-galaxy icon lexmapr-galaxy

LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms

miso-lims icon miso-lims

MISO: An open-source LIMS for NGS sequencing centres

qarrayrun icon qarrayrun

A helper tool for running array jobs on an HPC computational node.

rabbittclust icon rabbittclust

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

refchooser icon refchooser

Tools to help choose a reference from a list of assemblies.

rips icon rips

RIPS-Rapid Intuitive Pathogen Surveillance

serotools icon serotools

A toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping.

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