cgmlst
There are 16 repositories under cgmlst topic.
B-UMMI/chewBBACA
BSR-Based Allele Calling Algorithm
tseemann/cgmlst-dists
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
phac-nml/sistr_cmd
SISTR (Salmonella In Silico Typing Resource) command-line tool
jordanlab/STing
Ultrafast sequence typing and gene detection from NGS raw reads
BU-ISCIII/taranis
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
infinity-a11y/PhyloTrace
PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.
BCCDC-PHL/cgmlst-clustering
Scripts to support clustering of cgMLST allele profiles
BCCDC-PHL/kma-cgmlst
A cgMLST pipeline based on the KMA aligner
tripitakit/mlst2dist
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
bajicv/cgMLSTorg_scheme_scraper
cgMLST.org webpage scraper. Download and list available schemes from cgMLST.org, and find their versions and last modification date and time.
bajicv/enterobase_scheme_scraper
Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.
bajicv/pubMLST_scheme_scraper
rest.pubmlst.org webpage scraper. Download and list available schemes and profiles from PubMLST API, and find their last modification date using command line.
brueggemann-lab/pgl_cgmlst_2024
Repository for the pneumococcal cgMLST typing scheme (pneumococcal genome library)
Genomic-Medicine-Linkoping/JASEN
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
kriskiil/cgmlstsearch
Proof of concept implementation for indexed similarity search of a cgMLST profile against a database.
genpat-it/cgmlst-dists-py
The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann