(r39) Barrick Lab

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---+ <b><i>breseq</i></b>

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__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://barricklab.org/release/breseq/breseq_current.tar.gz][Current source code archive (version 0.24rc7) Jun 30 2014]]* |
| %ICON{download}% [[http://code.google.com/p/breseq/downloads/list][Previous versions (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 (200M)]] | 
| [[%ATTACHURL%/REL606.gbk.gz][%ICON{download}% Reference genome (REL606)]] |
| [[%ATTACHURL%/REL8593A_output][%ICON{external}% Example of __breseq__ output]] |

*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. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=24838886][&laquo;PubMed&raquo;]]

| *Download Link* | *Size* | *Description* |
| [[%ATTACHURL%/Clonal_Sample.tgz][%ICON{download}% <literal>Clonal_Sample.tgz</literal>]] | 267M | Input files for clonal sample |
| [[%ATTACHURL%/Clonal_Output.tgz][%ICON{download}% <literal>Clonal_Output.tgz</literal>]] | 1.2M | Output files for clonal sample |
| [[%ATTACHURL%/Population_Sample.tgz][%ICON{download}% <literal>Population_Sample.tgz</literal>]] | 1.4G | Input files for time-course of population samples |
| [[%ATTACHURL%/Population_Output.tgz][%ICON{download}% <literal>Population_Output.tgz</literal>]] | 11M | Output files for time-course of population samples, including comparison |
| [[%ATTACHURL%/Mutation_Examples.tgz][%ICON{download}% <literal>Mutation_Examples.tgz</literal>]] | 199K | Examples of using unassigned evidence to predict complex mutations |
| [[%ATTACHURL%/Poor_Evidence_Examples.tgz][%ICON{download}% <literal>Poor_Evidence_Examples.tgz</literal>]] | 139K | 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]].
Barrick Lab > ToolList > ToolsBacterialGenomeResequencing
Contributors to this topic
JeffreyBarrick, DanielDeatherage
Topic revision: r39 - 2014-06-30 - 23:22:50 - Main.JeffreyBarrick