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 Perl, 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.
Download:
Documentation:
Additional test data and an example of
breseq output:
Development versions are available from our public Mercurial repository:
Experimental (and outdated) double-clickable Installer, compatible only with Mac OS X 10.6:
Install details on various HPC systems:
Installation, Features, Methods, and Usage
Please see the HTML documentation included in the source archive downloads.
Feedback and Bug Reporting
Please send to
Jeffrey Barrick.
Contributors to this topic
JeffreyBarrick, DanielDeatherage
Topic revision: r32 - 2011-07-14 - 23:51:35 - Main.JeffreyBarrick