A tool for generating consensus long-read assemblies for bacterial genomes

A more efficient quality control tool for sequencing data

A tool for drawing ANI clustermap between all-vs-all microbial genomes

Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly

Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Pipeline for metabolic annotation of microbial genomes

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

A more intuitive version of du in rust

Download FASTQ files from SRA or ENA repositories.

Plasmid analysis using rearrangement distances

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Mummer alignment tool

Visualise and analyse nanopore (ONT) raw signals

This project is designed to find the potential modifications in bacterial genomes.

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

A Zotero plugin for syncing items and notes into Notion

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

zDB: comparative bacterial genomics made easy

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Bayesian inference of ancestral dates on bacterial phylogenetic trees

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Gene Absence Presence Identification tool.

Infer transmission clusters from SNP and timing data