Pinned Repositories
ARGprofiler
A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
argprofiler-paper-notebooks
Supporting notebooks for the ARGprofiler manuscript
ccphylo
cgemetagenomics
CGE metagenomics pipeline
CGPhylo
Core Genome Phylogenetics Tool
flankophile
kma
plasmidfinder
resfinder
SpanSeq
Center for Genomic Epidemiology's Repositories
genomicepidemiology/ARGprofiler
A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
genomicepidemiology/SpanSeq
genomicepidemiology/kma
genomicepidemiology/ccphylo
genomicepidemiology/plasmidfinder
genomicepidemiology/argprofiler-paper-notebooks
Supporting notebooks for the ARGprofiler manuscript
genomicepidemiology/cgemetagenomics
CGE metagenomics pipeline
genomicepidemiology/CGPhylo
Core Genome Phylogenetics Tool
genomicepidemiology/flankophile
genomicepidemiology/resfinder
genomicepidemiology/cgecore
genomicepidemiology/cgeisolate
CGE isolate pipeline
genomicepidemiology/CGELabs
CGELabs application for Great Life
genomicepidemiology/cgeutil
Generel utility tool for the Great Life Project
genomicepidemiology/fingerseq
genomicepidemiology/great-life
Guide to laptops and ONT software for the great-life project
genomicepidemiology/KMADBInspector
Tool for inspecting a KMA database and fetching stats related to homology of an input sample.
genomicepidemiology/kmergenetyper
Accurate Gene Typer
genomicepidemiology/ListPred
genomicepidemiology/outbreak_maker
Outbreak_maker
genomicepidemiology/probmap
Probabilistic mapper
genomicepidemiology/amrlmclustering
genomicepidemiology/cgevirus
Virus analysis cge
genomicepidemiology/fqgrep
genomicepidemiology/functional_testing
genomicepidemiology/kgt_mlst
kmergenetyper mlst parser
genomicepidemiology/livestock-amr-analysis
genomicepidemiology/NanoMGT
NanoMarkerGeneTyper
genomicepidemiology/pbs-torque-queue-considerate
genomicepidemiology/queue_decongestinator