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".
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Updated
Jan 10, 2022 - Shell
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".
Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system
Enterobase scheme scraper. Download and list available schemes from Enterobase, and find their last modification date and time.
multi-locus sequence type clade classifier for Clostridioides difficile
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
A companion application for analyzing and viewing BTyper output files in aggregate
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
Run mlst on multiple samples with integrated quality control.
A tool for conducting a gene screen on assemblies, producing an SRST2-like output.
Pathogen whole genome sequence (WGS) data analysis pipeline
cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
stringMLST datasets
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
In silico multi-locus sequence typing (MLST) for bacterial genomes
List and download schemes from pubMLST.org and other BIGSDB servers
MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
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