AlleleFinder

Last released Jul 18, 2025

None

confindr

Last released Feb 7, 2025

None

strainchoosr

Last released May 16, 2024

This package was originally created by Andrew Low. Now maintained by Adam Koziol.

MiSeqHashR

Last released Jun 22, 2023

OLCTools

Last released Feb 24, 2023

genemethods

Last released Nov 2, 2022

in-silico-pcr

Last released Oct 7, 2022

COWBAT

Last released May 20, 2022

CFIA OLC Workflow for Bacterial Assembly and Typing

sistr-cmd-olc

Last released May 17, 2022

Serovar predictions from Salmonella whole-genome sequence assemblies by determination of antigen geneand cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.

sipprverse

Last released Apr 21, 2022

Object oriented raw read typing software

AMR-Summary

Last released Apr 20, 2022

geneseekr

Last released Apr 13, 2022

genewrappers

Last released Apr 11, 2022

None

vsnpdev

Last released Jan 30, 2020

USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. SNP pipeline. Genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees.

validator_helper

Last released Nov 1, 2019

ftir-renamer

Last released Oct 21, 2019

File renamer for FTIR files

virus_typer

Last released Aug 9, 2019

GenomeQAML

Last released Jun 12, 2019

CFIA OLC Genome Quality Assessment with Machine Learning

fetagenome

Last released Mar 18, 2019

KubeJobSub

Last released Jan 21, 2019

sigseekr

Last released Dec 11, 2018

cowbathybrid

Last released Dec 6, 2018

plasmidextractor

Last released Feb 12, 2018