Introduction
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|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) <http://myxo.css.msu.edu/ecoli/>`_ [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|
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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 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239701>`_

See the :ref:`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.