National Microbiology Laboratory

Pinned Repositories

biohansel
Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
Language:Python26 15 537
ecoli_serotyping
In silico prediction of E. coli serotype
Language:Python48 8 2010
galaxy_tools
Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML
Language:Perl15 13 2725
irida
Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
Language:Java40 13 47231
mob-suite
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Language:Python118 12 14331
neptune
Neptune: Genomic Signature Discovery
Language:Python18 10 117
quasitools
Quasitools is a collection of tools for analysing viral quasispecies data.
Language:Python22 7 125
refseq_masher
Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
Language:Jupyter Notebook39 6 34
sistr_cmd
SISTR (Salmonella In Silico Typing Resource) command-line tool
Language:Python24 11 489
staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Language:Python116 7 12226

National Microbiology Laboratory's Repositories

phac-nml/ecoli_serotyping
In silico prediction of E. coli serotype
Language:Python48 8 2010
phac-nml/sistr_cmd
SISTR (Salmonella In Silico Typing Resource) command-line tool
Language:Python24 11 489
phac-nml/mikrokondo
A simple pipeline for bacterial assembly and quality control
Language:Nextflow12 6 382
phac-nml/irida-next
IRIDA Next
Language:Ruby8 6 1743
phac-nml/speciesabundance
Estimate the relative abundance of sequence reads originating from different species in a sample.
Language:Nextflow5 4 20
phac-nml/wade
WGS Analysis and Detection of Molecular Markers (WADE)
Language:R5 6 62
phac-nml/snvphylnfc
SNVPhyl nf-core Pipeline (Development)
Language:Nextflow3 4 71
phac-nml/arborator
Language:Python2 4 5
phac-nml/locidex
Common search engine for similarity based typing applications
Language:Python2 4 13
phac-nml/pipeline-standards
Guidelines for developing Nextflow pipelines for IRIDA Next.
2 5 111
phac-nml/profile_dists
Profile Dists: Convenient package for comparing genetic similarity of samples based on allelic profiles
Language:Python2 4 61
phac-nml/genomic_address_service
Package for clustering sequences de novo and assignment to existing nomenclature
Language:Python1 4 82
phac-nml/go-cluster
A utility for fast-matching and clustering.
Language:Go1 3 10
phac-nml/ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Language:Python1 3 10
phac-nml/pangonet
Create and manipulate SARS-CoV-2 pango lineages in a phylogenetic network.
Language:Python1 3 2
phac-nml/wade-data
Data for WGS Analysis and Detection of Molecular Markers (WADE)
Language:R1 4 01
phac-nml/arboratornf
EPS suite Arborator pipeline
Language:HTML
phac-nml/ArborView
A way to visualize beautiful phylogenetic trees alongside contextual data.
Language:HTML2 0
phac-nml/fastmatch-in
Fast matching for IRIDANext
Language:Nextflow3 0
phac-nml/gasclustering
Language:Nextflow4 4
phac-nml/gasnomenclature
Nomenclature assignment pipeline
Language:Nextflow4 0
phac-nml/inext_cli
IRIDA Next GraphQL Commandline toolkit
Language:Python3 2
phac-nml/irida-metadata-uploader
Language:Python
phac-nml/iridanextexample
An example pipeline for running on IRIDA Next
Language:Nextflow4 33
phac-nml/nf-pipelines
4 4
phac-nml/puppet-irida
The IRIDA module lets you use Puppet to install, deploy, and configure IRIDA web server (Alpha status)
Language:Puppet5 111
phac-nml/schedule-pipelines
Language:Python
phac-nml/staramrnf
nf-core StarAMR
Language:Nextflow4 7
phac-nml/viralassembly
Assemble and QC viral reads with a reference scheme
Language:Nextflow4 0
phac-nml/zebra-browser-print-wrapper
Language:JavaScript0 01