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 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.

Please see the HTML documentation included in the source code downloads for the most up-to-date information concerning installation, features, methods, and usage.

Download:

Current source code archive (Google Code)

Online 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

Feedback and Bug Reporting

Please report on Google Code or send to Jeffrey Barrick.