A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Java utilities for Bioinformatics

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

Text Only Genome Viewer!

Mining CRISPRs in Environmental Datasets

Code for phasing SVs with SNPs

EzAAI - High Throughput Prokaryotic AAI Calculator

Mapped QC analysis program

Java based tools for bulk downloading read/analysis files from ENA via FTP or Aspera.

A genome alignment and visualization system

Metagenomic Analysis in Real Time

Bacterial phylogenetics in BEAST 2.