breseq

Genetics

Software Description

1

Info

Module Name

breseq

Last Updated On

11/14/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html

Documentation

Software Description

From the breseq manual pages : 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

Agate Modules

Default

0.38.1-gcc-8.2.0-yipf7yn

Other Modules

0.38.1-gcc-8.2.0-yipf7yn, 0.26, 0.28, 0.28.1, 0.35.0, 0.36.0

Mangi Modules

Default

0.38.1-gcc-8.2.0-yipf7yn

Other Modules

0.38.1-gcc-8.2.0-yipf7yn, 0.26, 0.28, 0.28.1, 0.35.0, 0.36.0

Mesabi Modules

Default

0.38.1-gcc-8.2.0-yipf7yn

Other Modules

0.38.1-gcc-8.2.0-yipf7yn, 0.26, 0.28, 0.28.1, 0.35.0, 0.36.0