A tool for conducting a gene screen on assemblies, producing an SRST2-like output.

Scripts used to generate the analyses and figures in the paper "Systems-based approach for optimization of a scalable bacterial ST mapping assembly-free algorithm".

stringMLST datasets

Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.

multi-locus sequence type clade classifier for Clostridioides difficile

mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data

In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data

Run mlst on multiple samples with integrated quality control.

A companion application for analyzing and viewing BTyper output files in aggregate

MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.

Pathogen whole genome sequence (WGS) data analysis pipeline

Rapid, in silico characterization of Bacillus cereus group isolates using WGS data

Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.

Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system

Ultrafast sequence typing and gene detection from NGS raw reads

The MAB MLST Scheme for Mycobacterium absecssus

bacterial read typer 🧬 🛹 🦠

A collection of bioinformatics tools for use with galaxy written at Quadram Institute

In silico multi-locus sequence typing (MLST) for bacterial genomes