BSR-Based Allele Calling Algorithm
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Updated
Apr 29, 2024 - HTML
BSR-Based Allele Calling Algorithm
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
SISTR (Salmonella In Silico Typing Resource) command-line tool
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
Scripts to support clustering of cgMLST allele profiles
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
A cgMLST pipeline based on the KMA aligner
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
PubMLST.org webpage scraper. Download and list available schemes and profiles from PubMLST.org, 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.
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.
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