| Package Name | Access | Summary | Updated |
|---|---|---|---|
| in_silico_pcr | public | Perform in silico PCR analyses on FASTA- and/or FASTQ-formatted files | 2025-09-03 |
| stec_kma | public | No Summary | 2025-05-20 |
| azure_batch | public | AzureBatch is a Python-based suite of tools designed for the creation of pools, jobs and tasks in an Azure batch account | 2025-05-05 |
| skesa | public | Strategic Kmer Extension for Scrupulous Assemblies | 2025-03-25 |
| quast | public | Quality Assessment Tool for Genome Assemblies | 2025-03-25 |
| amr_summary | public | AMR Summary: a pipeline to identify AMR resistance genes located on plasmids by combining ResFinder and MOB-recon | 2025-03-25 |
| azure_storage | public | CFIA OLC Azure storage scripts | 2025-03-25 |
| allelefinder | public | Allele Tools | 2025-03-25 |
| confindr | public | Detect intra- and inter-species bacterial contamination in NGS reads | 2025-03-25 |
| cowsnphr | public | Single Nucleotide Variant Calling Pipeline | 2025-03-25 |
| seqsero2 | public | Salmonella serotype prediction from genome sequencing data | 2025-03-25 |
| sistr_cmd | public | 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. | 2025-03-25 |
| sigseekr | public | No Summary | 2025-03-25 |
| mob_suite | public | 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. | 2025-03-25 |
| virus_typer | public | Perform virus typing on Norovirus genogroups I and II, as well as Hepatitis A | 2025-03-25 |
| vsnp | public | vSNP - bacterial validation SNP analysis tool | 2025-03-25 |
| validator_helper | public | Package to help validate that CSVs outputted by your pipelines match up with what you think they should. | 2025-03-25 |
| genomeqaml | public | CFIA OLC Genome Quality Assessment with Machine Learning | 2025-03-25 |
| genewrappers | public | Python wrappers for bioinformatic tools | 2025-03-25 |
| genemethods | public | Common methods for object oriented gene target finding software | 2025-03-25 |
| cowbat | public | CFIA OLC Workflow for Bacterial Assembly and Typing | 2025-03-25 |
| geneseekr | public | Object oriented gene target finding software | 2025-03-25 |
| olctools | public | Python package for commonly used tools at OLC | 2025-03-25 |
| sipprverse | public | Object oriented raw read typing software | 2025-03-25 |
