Introduction

breseq (pronounced: breeze-seq) is a computational pipeline for the analysis of short-read re-sequencing data (e.g. 454, Illumina, SOLiD, 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 existing software programs are that it can:

1. Predict new sequence junctions, such as those associated with mobile element insertions, from single-end read data.
2. Reliably identify short indel mutations by appropriately masking the ends of read alignments.
3. Produce annotated output describing biologically relevant mutational events.

breseq has been used to analyze data from the Lenski long-term evolution experiment with E. coli [Barrick2009a][Barrick2009b].

breseq should be generally useful to researchers who are:

1. Following mutations over time in microbial evolution experiments.
2. Checking strains for 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.