(r32) Barrick Lab

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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 Perl, 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.

Download:
| %ICON{download}% [[http://code.google.com/p/breseq/downloads/list][Source code archive (Google Code)]] |
| %ICON{download}% [[http://%HTTP_HOST%/release/breseq/][Older versions (barricklab.org)]] |

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]] |

Development versions are available from our public Mercurial repository:
| [[http://%HTTP_HOST%/hg/breseq/archive/tip.tar.gz][%ICON{download}% Download Current Development Source Code Archive]] | 
| [[BreseqDevelopment][%ICON{gear}%  Breseq Developer Notes]] |
| [[http://%HTTP_HOST%/hg/breseq/][%ICON{info}% Browse Mercurial Repository]] |
| [[http://code.google.com/p/breseq/][%ICON{external}% Google Code Page]] | 

Experimental (and outdated) double-clickable Installer, compatible only with Mac OS X 10.6:
| [[http://barricklab.org/dist/breseq-0.0.1.dmg][%ICON{download}% Disk Image Installer, *breseq* version 0.01]] |

Install details on various HPC systems:
| [[BreseqInstallRanger][Installing on TACC Ranger]] |

---++ Installation, Features, Methods, and Usage

Please see the HTML documentation included in the source archive downloads.

---++ Feedback and Bug Reporting

Please send to [[mailto:jeffrey.e.barrick@gmail.com][Jeffrey Barrick]].
Barrick Lab > ToolList > ToolsBacterialGenomeResequencing
Contributors to this topic
JeffreyBarrick, DanielDeatherage
Topic revision: r32 - 2011-07-14 - 23:51:35 - Main.JeffreyBarrick