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.
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
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
A cgMLST pipeline based on the KMA aligner
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
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.
BSR-Based Allele Calling Algorithm
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)
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