BSR-Based Allele Calling Algorithm

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Collection of scripts for bacterial genomics

Fast k-mer based tool for multi locus sequence typing (MLST)

all methods related to Enterobase

Ultrafast sequence typing and gene detection from NGS raw reads

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

An easy way of MLSTyping your genomes in R.

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

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

List and download schemes from pubMLST.org and other BIGSDB servers

cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.

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

stringMLST datasets

bacterial read typer 🧬 🛹 🦠

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

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

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

Pathogen whole genome sequence (WGS) data analysis pipeline