An easy-to-use program to assign O1 Vibrio cholerae genomes to canonical lineages using phylogenetic placement.

The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples

Gotchas from the trenches of bioinformatics

MLSType from Enterobase Tool Kit

Subtyping of Francisella tularensis subtypes

Don’t Panic! Your Bacterial Genomics Handbook

Synteny and Rearrangement Identifier

A novel method for sequence similarity estimation

k-mers and the like

trapical: trapical rapidly aligns Pulsenet islolate core alleles

Antimicrobial Resistance Analysis

Genome browser and variant annotation

Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies

The Pathogenwatch MLST/cgMLST assignment tool

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

Fast implementation of the Neighbour-Joining method for phylogenetic inference

cloc counts blank lines, comment lines, and physical lines of source code in many programming languages.

SemiBin: metagenomics binning with self-supervised deep learning

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

tool to determine optimal refrerence genome given a set of fasta files

Common search engine for similarity based typing applications

🐪Classification through yAML Heuristic Mapping Protocol 🐪

A list of interesting genome browser and genome visualization programs

The R Installation Manager

ntHash implementation in Rust

A Core Genome MLST (cgMLST) Typing Tool