(r51) 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 haploid 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 and Cygwin. 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.

---++ Comprehensive Analysis of Mutations in Evolved Microbes Using _breseq_
*ASM Microbe 2021 On-Demand Workshop (June 20-24)*

*Jeffrey Barrick (UT Austin)* %BR% Introduction: Identifying Mutations and Studying Microbial Genome Evolution with breseq %BR% [[%ATTACHURL%/ASM_Microbe_2021_slides_Barrick.pdf][%ICON{pdf}% Download Slides]]

<a href="https://forms.gle/qkvkjbqCXZAhY7GW6"><img height="300" src="%ATTACHURL%/breseq_survey.png"><br><br><font size="+1">Interested in getting help using <i>breseq</i>? Fill out the Interactive Workshop Survey.</font></a>

---++ Resources

*Online Documentation:*
| [[%ATTACHURL%/documentation][%ICON{viewtopic}% Online __breseq__ documentation]] |

*Download:*
| %ICON{download}% | [[https://github.com/barricklab/breseq/releases/latest][Latest version from GitHub]] |

*Previous Versions:*
| %ICON{download}% [[http://barricklab.org/release/breseq][Previous versions from 0.24rc6 to 0.25d (barricklab.org)]] |
| %ICON{download}% [[http://code.google.com/p/breseq/downloads/list][Previous versions up to 0.24rc6 (Google Code)]] |

*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]] |

---++ Feedback and Bug Reporting

Please report bugs on [[https://github.com/barricklab/breseq/issues][GitHub]].

---++ 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 |
Barrick Lab > ToolList > ToolsBacterialGenomeResequencing
Contributors to this topic
JeffreyBarrick, DanielDeatherage
Topic revision: r51 - 2021-05-31 - 14:34:46 - Main.JeffreyBarrick