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.
Additional test data and an example of breseq output:
Tutorial input and results files for breseq book chapter
, Barrick, J.E.
. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
. Methods Mol. Biol. 1151
Feedback and Bug Reporting
Please report bugs on Google Code
or send to Jeffrey Barrick