A toolkit for prokaryotic comparative genomics

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

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

A tool to generate a JSON diff between two GFF files, written in Rust

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

The lean application framework for Python. Build sophisticated user interfaces with a simple Python API. Run your apps in the terminal and a web browser.

A command line tool that draw plots on the terminal.

Synteny and Rearrangement Identifier

Methods and classes to support Biosynthetic Gene Cluster analysis

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

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

A collection of themes for RStudio

🚀 A sequencing simulator

Snakemake pipeline for simulating shotgun metagenomic samples

CAMISIM: Simulating metagenomes and microbial communities

zDB: comparative bacterial genomics made easy

Fast and space-efficient taxonomic classification of long reads

Automatically exported from code.google.com/p/figtree

Accelerated BLAST compatible local sequence aligner.

Convert genbank files to a swath of other formats

Estimate metagenomic coverage and sequence diversity

Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at the Jackson Laboratory.

Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes