Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)
-
Updated
May 30, 2024 - Python
Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
BSR-Based Allele Calling Algorithm
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
SISTR (Salmonella In Silico Typing Resource) command-line tool
cgMLST.org webpage scraper. Download and list available schemes from cgMLST.org, and find their versions and last modification date and time.
Scripts to support clustering of cgMLST allele profiles
A cgMLST pipeline based on the KMA aligner
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
Proof of concept implementation for indexed similarity search of a cgMLST profile against a database.
Add a description, image, and links to the cgmlst topic page so that developers can more easily learn about it.
To associate your repository with the cgmlst topic, visit your repo's landing page and select "manage topics."