mlst
There are 29 repositories under mlst topic.
B-UMMI/chewBBACA
BSR-Based Allele Calling Algorithm
achtman-lab/GrapeTree
GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
kjolley/BIGSdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
aleimba/bac-genomics-scripts
Collection of scripts for bacterial genomics
jordanlab/stringMLST
Fast k-mer based tool for multi locus sequence typing (MLST)
zheminzhou/EToKi
all methods related to Enterobase
jordanlab/STing
Ultrafast sequence typing and gene detection from NGS raw reads
iferres/MLSTar
An easy way of MLSTyping your genomes in R.
lmc297/BTyper3
In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data
SegataLab/metamlst
MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
Public-Health-Bioinformatics/pubmlst_client
List and download schemes from pubMLST.org and other BIGSDB servers
lmc297/seq2mlst
In silico multi-locus sequence typing (MLST) for bacterial genomes
BU-ISCIII/taranis
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
lmc297/BTyper
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
jordanlab/stringMLST_datasets
stringMLST datasets
tomdstanton/bart
bacterial read typer :dna: :skateboard: :microbe:
quadram-institute-bioscience/galaxy-tools
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
CFSAN-Biostatistics/cronology
cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.
wanyuac/geneDetector
A tool for conducting a gene screen on assemblies, producing an SRST2-like output.
xiaoli-dong/pathogenseq
Pathogen whole genome sequence (WGS) data analysis pipeline
BCCDC-PHL/mlst-nf
Run mlst on multiple samples with integrated quality control.
lmc297/BMiner
A companion application for analyzing and viewing BTyper output files in aggregate
tripitakit/mlst2dist
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
bajicv/enterobase_scheme_scraper
Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.
eliottBo/MLSTclassifier_cd
multi-locus sequence type clade classifier for Clostridioides difficile
Genomic-Medicine-Linkoping/JASEN
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
npavlovikj/MLST_stringMLST_analyses
Scripts used to generate the analyses and figures in the paper "Systems-based approach for optimization of a scalable bacterial ST mapping assembly-free algorithm".
phac-nml/mab_mabscessus
The MAB MLST Scheme for Mycobacterium absecssus
Public-Health-Bioinformatics/irida-plugin-mlst
Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system