Introduction¶
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:
- Accurately predict new sequence junctions, such as those associated with mobile element insertions.
- Integrate multiple sources of evidence for genetic changes into mutation predictions.
- 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:
- Tracking mutations over time in microbial evolution experiments.
- Checking strains for unwanted second-site mutations after genetic manipulations.
- Identifying mutations that occur during strain improvement or after long-term culture of engineered strains.
- 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.
