breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R. More information at
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Latest commit 62dc24e Feb 17, 2017 @jeffreybarrick jeffreybarrick Fixed problem with breseq creating SUB mutation types that are 'media…
…ted' but rejecting them when used as input files.
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aux_build/m4 Changed datadir in breseq to be relative to binbir so as preparation … Mar 6, 2015
extern updates to Makefiles to get proper library linking Oct 25, 2016
ports Updated to v0.24, but not ready for release; changed junctions to pre… Aug 6, 2013
src Fixed problem with breseq creating SUB mutation types that are 'media… Feb 17, 2017
tests Update to bowtie2 settings... breaks consistency a small amount, poss… Jan 19, 2017
.gitignore Fix for SAM file input, update of MOB test annotation for negative du… Nov 9, 2016
AUTHORS Updated to v0.24, but not ready for release; changed junctions to pre… Aug 6, 2013
COPYING Updated to v0.24, but not ready for release; changed junctions to pre… Aug 6, 2013
ChangeLog Updated ChangeLog and version for v0.30.0 Feb 11, 2017
DEVELOPER Updated to v0.24, but not ready for release; changed junctions to pre… Aug 6, 2013
LICENSE first try at binary production script; incremented version to 0.24d Mar 8, 2015
Makefile.am Fixed removing .DS_Store files for discheck Dec 20, 2016
NEWS Updated to v0.24, but not ready for release; changed junctions to pre… Aug 6, 2013
README Updating docs Mar 20, 2015
README-BINARY Fixed binary dist test to clean itself before running so that it can … Mar 13, 2015
README.md edited readme down to link Nov 23, 2015
binarydist.sh Fixed problem with MacOSX 10.7 compatible compile where INFs in polym… Nov 12, 2016
bootstrap.sh Updated to v0.24, but not ready for release; changed junctions to pre… Aug 6, 2013
configure.ac Updated ChangeLog and version for v0.30.0 Feb 11, 2017