A genome visualization python package for comparative genomics
Rapid comparison and dereplication of genomes
microbiome R package
Build a partitioned pangenome graph from microbial genomes
Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python
PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
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.
Rapid determination of appropriate reference genomes.
An easy-to-use C++ application to count bacterial colonies (i.e. CFU).
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
Collection of commonly used RDP Tools for easy building
BRIG is a cross-platform (Windows/Mac/Linux) application that displays circular comparison images of multiple genomes using BLAST.
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.
📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria
scripts and notes for learning
Metagenomic pipeline and other general scripts used in the lab.
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