breseq

Welcome to the breseq user manual!

breseq is a computational pipeline for finding mutations in haploid microbial genomes by comparing short-read re-sequencing data to an already sequenced reference genome. See the Introduction for a full description of what breseq does and when to use it.

New to breseq? Start with Installation and then walk through the Test Drive example.

Looking to contribute to breseq itself? See CONTRIBUTING.md on GitHub.