Collection of scripts for bacterial genomics
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Updated
Dec 6, 2019 - Perl
Collection of scripts for bacterial genomics
BSR-Based Allele Calling Algorithm
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
An easy way of MLSTyping your genomes in R.
Fast k-mer based tool for multi locus sequence typing (MLST)
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
In silico multi-locus sequence typing (MLST) for bacterial genomes
List and download schemes from pubMLST.org and other BIGSDB servers
Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
A companion application for analyzing and viewing BTyper output files in aggregate
Pathogen whole genome sequence (WGS) data analysis pipeline
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.
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