Proof of concept implementation for indexed similarity search of a cgMLST profile against a database.
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Updated
Sep 30, 2019 - Python
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
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
Scripts to support clustering of cgMLST allele profiles
cgMLST.org webpage scraper. Download and list available schemes from cgMLST.org, and find their versions and last modification date and time.
SISTR (Salmonella In Silico Typing Resource) command-line tool
The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.
rest.pubmlst.org webpage scraper. Download and list available schemes and profiles from PubMLST API, and find their last modification date using command line.
Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)
A cgMLST pipeline based on the KMA aligner
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
BSR-Based Allele Calling Algorithm
PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.
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