BSR-Based Allele Calling Algorithm

🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables

SISTR (Salmonella In Silico Typing Resource) command-line tool

Ultrafast sequence typing and gene detection from NGS raw reads

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

PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.

A cgMLST pipeline based on the KMA aligner

Scripts to support clustering of cgMLST allele profiles

Proof of concept implementation for indexed similarity search of a cgMLST profile against a database.

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

rest.pubmlst.org webpage scraper. Download and list available schemes and profiles from PubMLST API, and find their last modification date using command line.

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

The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann

Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)

cgMLST.org webpage scraper. Download and list available schemes from cgMLST.org, and find their versions and last modification date and time.

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