# breseq

## Summary

+ **Module Name:** breseq
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html](http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html)

## Software Description

From the [breseq manual
pages](http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html)
: 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: Predict new sequence junctions, such as those
associated with mobile element insertions, from single-end read data.
Reliably identify short indel mutations by appropriately masking the
ends of read alignments. Produce annotated output describing
biologically relevant mutational events. breseq is available on the lab
cluster.
## General Linux

To load this module for use in a Linux environment, you can run the command:

	module load breseq

Depending on where you are working, there may be more than one version of breseq available.
To see which modules are available for loading you can run:

	module avail breseq