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 Latest version from GitHub

Previous Versions:

download Previous versions from 0.24rc6 to 0.25d (
download Previous versions up to 0.24rc6 (Google Code)

Online Documentation:

viewtopic Online breseq documentation

Additional test data and an example of breseq output:

download FASTQ reads for E. coli strain REL8593A (200M)
download Reference genome (REL606)
external 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»

Download Link Size Description
download Clonal_Sample.tgz 267M Input files for clonal sample
download Clonal_Output.tgz 1.2M Output files for clonal sample
download Population_Sample.tgz 1.4G Input files for time-course of population samples
download Population_Output.tgz 11M Output files for time-course of population samples, including comparison
download Mutation_Examples.tgz 199K Examples of using unassigned evidence to predict complex mutations
download Poor_Evidence_Examples.tgz 139K Example output showing characteristics of poor evidence

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Topic revision: r48 - 23 Nov 2015 - 14:52:51 - JeffreyBarrick
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