📊 Circular and Rectangular Manhattan Plot

Visualize and annotate genomic coverage with ggplot2

Benchmarking adapter and quality trimming tools

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

snipit: summarise snps relative to your reference sequence

D3.js based visualizations of cobrapy metabolic models

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

geNomad: Identification of mobile genetic elements

A tool to optimize real world problems

Inferring global and local strict molecular clocks using root-to-tip regression

A grammar of graphics for comparative genomics

A tool for removing redundant genomes from a set of assemblies

Scripts to analyse within-host evolution during S. aureus colonisation and infection

fast phage annotation program

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

A tool to find sequencing data and metadata from public databases.

A tool to circularize genome assemblies

structural variant calling and genotyping with existing tools, but, smoothly.

Structural variation caller using third generation sequencing

Useful bash one-liners for bioinformatics.

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.

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

Fast genome-wide functional annotation through orthology assignment

SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.

An updated pipeline for pangenome investigation