breseq (pronounced: \brēz-ˈsēk\ or breeze-seq) is a computational pipeline for the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent, etc.). It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome. breseq is intended for microbial genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from the reference sequence (<1 mutation per 1000 bp).

breseq’s primary advantages over other software programs are that it can:

  1. Accurately predict new sequence junctions, such as those associated with mobile element insertions.

  2. Integrate multiple sources of evidence for genetic changes into mutation predictions.

  3. Produce annotated output describing biologically relevant mutational events.

breseq was initially developed to analyze data from the Lenski long-term evolution experiment with E. coli (Link to LTEE Website) [Barrick2009a] [Barrick2009b].

However, breseq may be generally useful to researchers who are:

  1. Tracking mutations over time in microbial evolution experiments.

  2. Checking strains for unwanted second-site mutations after genetic manipulations.

  3. Identifying mutations that occur during strain improvement or after long-term culture of engineered strains.

  4. Discovering what mutations arise in pathogens during infection or cause antibiotic resistance.

Citing breseq

Please cite the main breseq publication if you use this software in your research:

  • 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. Link to Full Text

See the Annotated bibliography for a full list of papers that describe breseq. We appreciate you also citing these publications if they are relevant for your application.