<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 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][«PubMed»]] | *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 |
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Topic revision: r51 - 2021-05-31 - JeffreyBarrick