LexicMap: efficient sequence alignment against millions of prokaryotic genomes

👁️ Python library to plot DNA sequence features (e.g. from Genbank files)

RNAseq analysis notes from Ming Tang

Plotting scripts for long read sequencing data

CAMISIM: Simulating metagenomes and microbial communities

Pan-genome wide association studies

Scripts for running antismash on calc

A toolkit for prokaryotic comparative genomics

Reaction Analysis through Imaging of Chemical Units

Presentation-Ready Data Summary and Analytic Result Tables

Orchestrating Microbiome Analysis

BGCViz - a shiny web app, which uses genomic coordinates of BGCs from different sources for a comprehensive comparison.

antiSMASH

A set of Cytoscape tutorials for my students

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Make sankey, alluvial and sankey bump plots in ggplot

(Meta-)genome screening for functional and natural product gene sequences

Workflow to assign Taxonomy to a bacteriophage genome isolate

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Calculate fastq reads and sequencing coverage

CarveMe: genome-scale metabolic model reconstruction

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads

📖 For those who wanna learn Bash

🆔 Scan contig files against PubMLST typing schemes

Parse NCBI CD-search results to find and visualise the domain architecture of secondary metabolite synthases

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.