| allelefinder | 0.4.7 | Allele Tools | Mar 25, 2025 | MIT |
| amr_summary | 0.0.1 | AMR Summary: a pipeline to identify AMR resistance genes located on plasmids by combining ResFinder and MOB-recon | Mar 25, 2025 | MIT |
| azure_batch | 0.0.13 | AzureBatch is a Python-based suite of tools designed for the creation of pools, jobs and tasks in an Azure batch account | May 5, 2025 | MIT |
| azure_storage | 0.0.14 | CFIA OLC Azure storage scripts | Mar 25, 2025 | MIT |
| confindr | 0.8.1 | Detect intra- and inter-species bacterial contamination in NGS reads | Mar 25, 2025 | MIT |
| cowbat | 0.5.0.12 | CFIA OLC Workflow for Bacterial Assembly and Typing | Mar 25, 2025 | MIT |
| cowsnphr | 0.0.38 | Single Nucleotide Variant Calling Pipeline | Mar 25, 2025 | MIT |
| genemethods | 0.0.0.59 | Common methods for object oriented gene target finding software | Mar 25, 2025 | MIT |
| geneseekr | 0.5.0 | Object oriented gene target finding software | Mar 25, 2025 | MIT |
| genewrappers | 0.0.0.12 | Python wrappers for bioinformatic tools | Dec 18, 2025 | MIT |
| genomeqaml | 0.0.14 | CFIA OLC Genome Quality Assessment with Machine Learning | Mar 25, 2025 | MIT |
| in_silico_pcr | 0.0.3.7 | Perform in silico PCR analyses on FASTA- and/or FASTQ-formatted files | Jan 19, 2026 | MIT |
| mob_suite | 3.0.3 | This package MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies. | Mar 25, 2025 | Apache License, Version 2.0 |
| olcnastools | 1.3.0 | OLC NAS tools | Jan 22, 2026 | MIT |
| olctools | 1.3.9 | Python package for commonly used tools at OLC | Mar 11, 2026 | MIT |
| quast | 5.1.0 | Quality Assessment Tool for Genome Assemblies | Mar 25, 2025 | Custom |
| seqsero2 | 1.2.1 | Salmonella serotype prediction from genome sequencing data | Mar 25, 2025 | GPLv2 |
| sigseekr | 0.2.4 | — | Mar 25, 2025 | MIT |
| sipprverse | 0.2.49 | Object oriented raw read typing software | Mar 25, 2025 | MIT |
| sistr_cmd | 1.1.3 | Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction. This version has requirements pinned to be compatible with the CFIA COWBAT pipeline. Please use the bioconda version. | Mar 25, 2025 | Apache |
| skesa | 2.4.0 | Strategic Kmer Extension for Scrupulous Assemblies | Mar 25, 2025 | Public Domain |
| stec_kma | 2025.05.20.1 | — | May 20, 2025 | MIT |
| validator_helper | 0.0.10 | Package to help validate that CSVs outputted by your pipelines match up with what you think they should. | Mar 25, 2025 | MIT |
| virus_typer | 0.0.0.3 | Perform virus typing on Norovirus genogroups I and II, as well as Hepatitis A | Mar 25, 2025 | MIT |
| vsnp | 0.0.20 | vSNP - bacterial validation SNP analysis tool | Mar 25, 2025 | — |
