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

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

Ultrafast sequence typing and gene detection from NGS raw reads

An easy way of MLSTyping your genomes in R.

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

EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for clinical microbiology, outbreak investigations, and genomic research.

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.

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

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

stringMLST datasets

bacterial read typer :dna: :skateboard: :microbe:

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

Ultra-fast SNP/indel-level distance calculator for core genome MLST analysis in bacterial genomics

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

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

Pathogen whole genome sequence (WGS) data analysis pipeline

Chlamydia trachomatis Genome Assembly Pipeline

Run mlst on multiple samples with integrated quality control.

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

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

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".

multi-locus sequence type clade classifier for Clostridioides difficile

Fast allele caller for cgMLST/wgMLST schemas, compatible with chewBBACA. 12-17x faster with SIMD Smith-Waterman (parasail).

Microbiome