Welcome to bfast. **This repository is no longer maintained. You should really not use this unless you have SOLiD sequencing data, which has not been generated for a long time. Please use other aligners like bwa, bowtie, etc. Issues and pull requests will be ignored.** bfast is copyrighted software. Please see the file LICENSE for details. For manual pages, including installation directions, please see: manual/bfast-book.pdf