Pinned Repositories
core-phylogenomics
Pipeline for identifying core SNPs and building a phylogenetic tree
galaxy-hackathon-2014
genomics-data-index
Indexes genomes using SNVs, MLST, or kmers for rapid querying, clustering, and visualization.
microbial-informatics-2014
Microbial Whole Genome Sequence data analysis labs for 2014
nf-core-assemblyexample
orthomcl-pipeline
Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
snvphyl-galaxy
card-live-dashboard
irida
Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
apetkau's Repositories
apetkau/genomics-data-index
Indexes genomes using SNVs, MLST, or kmers for rapid querying, clustering, and visualization.
apetkau/nf-core-assemblyexample
apetkau/nf-core-genomicnomenclature
apetkau/assembly-nf
apetkau/cardlive-presentation-2020
apetkau/ggtree-tutorial
apetkau/nf-core-mlstprofiler
apetkau/nf-core-pathoidentification
apetkau/2022-01-26-Downloading-and-assembling-microbial-sequence-data
Repository for January 26, 2022 "Downloading and assembling microbial sequence data" Workshop by Aaron Petkau
apetkau/bioconda-recipes
Conda recipes for the bioconda channel.
apetkau/EToKi
all methods related to Enterobase
apetkau/fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases
apetkau/from-samplesheet-test-nf
apetkau/genomics-data-index-evaluation
apetkau/genomics-data-index-evaluation-manuscript
apetkau/genomics-data-index-examples
Documentation and example code for an index of SNVs, kmers, and MLST (genomics-data-index).
apetkau/irida
Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
apetkau/irida-plugin-species-abundance
Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system
apetkau/nextflow
A DSL for data-driven computational pipelines
apetkau/nextflow-plugins
Nextflow plugins index repository
apetkau/nf-core-assemblyexample2
apetkau/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
apetkau/nf-core-queryprofiles
apetkau/nf-hello
Nextflow plugin implementation skeleton
apetkau/nf-plugins-test
apetkau/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
apetkau/test-security-scanning
apetkau/tools-iuc
Tool Shed repositories maintained by the Intergalactic Utilities Commission
apetkau/training-material
A collection of Galaxy-related training material
apetkau/vtec-workshop-2023