breseq
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.
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