microbiome R package

A genome visualization python package for comparative genomics

Rapid comparison and dereplication of genomes

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.

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.

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

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 commonly used RDP Tools for easy building

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.

scripts and notes for learning

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

Metagenomic pipeline and other general scripts used in the lab.

creating hybrid-gene phylogenetic trees for diversity analyses

A MALDI Mass Spectrometry Bioinformatics Platform

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

The NFDI4Microbiota Knowledge Base