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.

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Release versions:

Release	Date
breseq-0.10, Source Code Archive	June 6, 2011
breseq-1.00 Release Candidate 8, Source Code Archive	April 26, 2011
breseq-1.00 Release Candidate 7, Source Code Archive	April 9, 2011
breseq-1.00 Release Candidate 6, Source Code Archive	March 28, 2011
breseq-1.00 Release Candidate 5, Source Code Archive	March 5, 2011
breseq-1.00 Release Candidate 4, Source Code Archive	October 31, 2010
breseq-1.00 Release Candidate 3, Source Code Archive	October 21, 2010
breseq-1.00 Release Candidate 2, Source Code Archive	October 19, 2010
breseq-1.00 Release Candidate 1, Source Code Archive	October 17, 2010

See all release versions.

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 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.