(r46) 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.

%BLUE% NEW: Precompiled binaries are now available for MacOSX and Linux x86_64!%ENDCOLOR% %BR%
Update: Path error in Linux binary distribution fixed Mar 19 2015

*Download:*
| %ICON{download}% *[[http://barricklab.org/release/breseq/breseq_current.tar.gz][Current source code archive (version 0.25d) Mar 8 2015]]* |
| %ICON{download}% *[[http://barricklab.org/release/breseq/breseq-current-Darwin-universal.tar.gz][Current MacOSX universal binary (version 0.25d) Mar 8 2015]]* |
| %ICON{download}% *[[http://barricklab.org/release/breseq/breseq-current-Linux-x86_64.tar.gz][Current Linux x86_64 binary (version 0.25d) Mar 8 2015]]* |

*Previous Versions:*
| %ICON{download}% [[http://barricklab.org/release/breseq][Previous versions after 0.24rc6 (barricklab.org)]] |
| %ICON{download}% [[http://code.google.com/p/breseq/downloads/list][Previous versions up to 0.24rc6 (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: r46 - 2015-03-19 - 19:20:55 - Main.JeffreyBarrick