<noautolink> <!-- * Set PAGETITLE = Barrick Lab :: breseq --> ---+ <b><i>breseq</i></b> <div style="float: right; margin:10px;"><img style="border-color: black; border-style: solid; border-width: 1px;" src="%PUBURL%/%WEB%/ToolList/breseq_icon.gif"></div> __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 <nop>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. *Download:* | %ICON{download}% [[http://code.google.com/p/breseq/downloads/list][Current source code archive (Google Code)]] | *Online Documentation:* | [[%ATTACHURL%/documentation][%ICON{viewtopic}% online *breseq* documentation]] | *Additional test data and an example of __breseq__ output:* | [[%ATTACHURL%/REL8593A.fastq.gz][%ICON{download}% FASTQ reads for _E. coli_ strain REL8593A (200 Mb)]] | | [[%ATTACHURL%/REL606.gbk.gz][%ICON{download}% reference genome (REL606)]] | | [[%ATTACHURL%/REL8593A_output][%ICON{external}% example of *breseq* output]] | *Tutorial input and results files for upcoming __Methods in Molecular Biology__ chapter:* | [[%ATTACHURL%/Clonal_Sample.tgz][%ICON{download}% <literal>Clonal_Sample.tgz</literal>]] | Input files for clonal sample | | [[%ATTACHURL%/Population_Sample.tgz][%ICON{download}% <literal>Population_Sample.tgz</literal>]] | Input files for time-course of population samples | | [[%ATTACHURL%/Mutation_Examples.tgz][%ICON{download}% <literal>Mutation_Examples.tgz</literal>]] | Examples of using unassigned evidence to predict complex mutations | | [[%ATTACHURL%/Poor_Evidence_Examples.tgz][%ICON{download}% <literal>Poor_Evidence_Examples.tgz</literal>]] | Example output showing characteristics of poor evidence | ---++ Feedback and Bug Reporting Please report bugs on [[http://code.google.com/p/breseq/issues/list][Google Code]] or send to [[mailto:jeffrey.e.barrick@gmail.com][Jeffrey Barrick]].
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JeffreyBarrick, DanielDeatherage
Topic revision: r35 - 2013-08-14 - 16:33:17 - Main.JeffreyBarrick
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