breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. breseq is a command line tool implemented in Perl, C++, and R. It will compile and function on a variety of Unix platforms, including MacOSX. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.

Download:

Source code archive (Google Code)

Older versions (barricklab.org)

Documentation:

online breseq documentation

Additional test data and an example of breseq output:

FASTQ reads for E. coli strain REL8593A (200 Mb)

reference genome (REL606)

example of breseq output

Development versions are available from our public Mercurial repository:

Download Current Development Source Code Archive

Breseq Developer Notes

Browse Mercurial Repository

Google Code Page

Experimental (and outdated) double-clickable Installer, compatible only with Mac OS X 10.6:

Disk Image Installer, breseq version 0.01

Install details on various HPC systems:

Installation, Features, Methods, and Usage

Please see the HTML documentation included in the source archive downloads.

Feedback and Bug Reporting

Please send to Jeffrey Barrick.