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.

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

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

creating hybrid-gene phylogenetic trees for diversity analyses

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

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

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

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

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

MGKit: Metagenomics Framework

Bacterial video tracking & analysis

GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

SPIRO is a Smart Plate Imaging Robot

Code to go with the https://doi.org/10.1101/271569 publication. Downloads html pages from culture-collection centers and mines these for growth temperature data.

Pipelines dealing with high throughput sequencing data for microbiology diagnostic procedures. Documentation available at http://metagenlabdiag-pipelines.readthedocs.io/en/latest/ and Docker images at https://hub.docker.com/r/metagenlab/diag_pipelines/.