Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.
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Updated
May 4, 2024 - R
Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.
Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)
The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann
rest.pubmlst.org webpage scraper. Download and list available schemes and profiles from PubMLST API, and find their last modification date using command line.
Proof of concept implementation for indexed similarity search of a cgMLST profile against a database.
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.
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
Scripts to support clustering of cgMLST allele profiles
A cgMLST pipeline based on the KMA aligner
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
SISTR (Salmonella In Silico Typing Resource) command-line tool
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
BSR-Based Allele Calling Algorithm
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