microbiome R package

Rapid comparison and dereplication of genomes

A genome visualization python package for comparative genomics

Build a partitioned pangenome graph from microbial genomes

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Rapid determination of appropriate reference genomes.

An easy-to-use C++ application to count bacterial colonies (i.e. CFU).

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

Collection of commonly used RDP Tools for easy building

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

Collection of scripts for bacterial genomics

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

Metagenomic pipeline and other general scripts used in the lab.

scripts and notes for learning

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

A MALDI Mass Spectrometry Bioinformatics Platform

creating hybrid-gene phylogenetic trees for diversity analyses

hAMRoaster is an analysis pipeline that can compare the output of nine different tools for detecting AMR genes and provide metrics of their performance

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.