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.

NEW: Precompiled binaries are now available for MacOSX and Linux x86_64!
Update: Path error in Linux binary distribution fixed Mar 19 2015


download Current source code archive (version 0.25d) Mar 8 2015
download Current MacOSX universal binary (version 0.25d) Mar 8 2015
download Current Linux x86_64 binary (version 0.25d) Mar 8 2015

Previous Versions:

download Previous versions after 0.24rc6 (
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

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

Feedback and Bug Reporting

Please report bugs on Google Code or send to Jeffrey Barrick.

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Topic revision: r46 - 19 Mar 2015 - 19:20:55 - Main.JeffreyBarrick
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