is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid 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 and Cygwin. 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.
Additional test data and an example of breseq output:
Feedback and Bug Reporting
Please report bugs on GitHub
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