breseq
breseq 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.
Download:
Previous Versions:
Online Documentation:
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
Deatherage, D.E.,
Barrick, J.E.. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using
breseq.
Methods Mol. Biol. 1151:165-188.
«PubMed»