breseq
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.
breseq is a command line tool implemented in C++ and R. It will compile and function on a variety of Unix platforms, including MacOSX. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.
Please see the HTML documentation included in the source code downloads for the most up-to-date information concerning installation, features, methods, and usage.
NEW: Precompiled binaries are now available for MacOSX and Linux x86_64!
Download:
Previous Versions:
Online Documentation:
Additional test data and an example of breseq output:
Feedback and Bug Reporting
Please report bugs on
GitHub or send to
Jeffrey Barrick.
Tutorial input and results files for breseq book chapter
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.
«PubMed»
Contributors to this topic
JeffreyBarrick, DanielDeatherage
Topic revision: r47 - 2015-03-21 - 14:19:13 - Main.JeffreyBarrick