Bowtie: Other tools

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title>Bowtie: Other tools</title> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <link rel="stylesheet" type="text/css" href="css/style.css" media="screen" /> <meta name="verify-v1" content="YJT1CfXN3kzE9cr+jvNB+Q73lTfHrv8eivoY+xjblc0=" /> </head> <body> <div id="wrap"> <div id="top"> <div class="lefts"> <table width="100%" cellpadding="2"> <tr> <td align="left" valign="middle" width="145"> <a href="./index.shtml"><img style="padding-left: 7pt; padding-top: 6pt" height="65" src="images/bowtie_logo.png"/></a> </td> <td align="left" valign="top"> <a href="./index.shtml"><h1>Bowtie</h1></a> <h2>An ultrafast memory-efficient short read aligner</h2> </td> <td align="right" valign="middle"> <a href="http://www.jhu.edu/"><img style="padding-top: 7pt; padding-right: 7pt" border=0 height="55" src="images/university.small.horizontal.white.png"></a> </td> </tr> </table> </div> </div> <div id="main"> <div id="rightside" style="padding-left: 20px"> <h2>Site Map</h2> <div class="box"> <ul> <li><a href="index.shtml">Home</a></li> <li><a href="news.shtml">News archive</a></li> <li><a href="tutorial.shtml">Getting started</a></li> <li><a href="manual.shtml">Manual</a></li> <li><a href="other_tools.shtml">Tools that use Bowtie</a></li> </ul> </div> <h2><u>Latest Release</u></h2> <div class="box"> <ul> <table width="100%"> <tr> <td colspan="2"><a href="http://bioconda.github.io/recipes/bowtie/README.html"><img src="https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square"/></a></td> </tr> <tr> <td> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.1">Bowtie 1.3.1</a> </td> <td align="right"> 09/13/21 </td> </tr> <tr> <td colspan=2> <li style="font-size: x-small; line-height: 130%">Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. <a href="http://genomebiology.com/2009/10/3/R25">Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>. <i><a href="http://genomebiology.com">Genome Biol</a></i> 10:R25. </td> </tr> <tr> <td colspan=2> <li style="font-size: x-small; line-height: 130%">For release updates, subscribe to the <a href="https://lists.sourceforge.net/lists/listinfo/bowtie-bio-announce">mailing list</a>. </td> </tr> </table> </ul> </div> <h2>Links</h2> <div class="box"> <ul> <li><a href="https://github.com/BenLangmead/bowtie">Bowtie GitHub repository</a></li> <li><a href="https://github.com/BenLangmead/bowtie/issues">Report an issue</a></li>  </ul> </div> <h2>Related Tools</h2> <div class="box"> <ul> <table width="100%"> <tr> <td> <a href="./bowtie2/index.shtml">Bowtie 2</a>: Fast, accurate read alignment </td> </tr> <tr> <td> <a href="./crossbow/index.shtml">Crossbow</a>: Genotyping, cloud computing </td> </tr> <tr> <td> <a href="http://tophat.cbcb.umd.edu">Tophat</a>: RNA-Seq splice junction mapper </td> </tr> <tr> <td> <a href="http://cufflinks.cbcb.umd.edu">Cufflinks</a>: Isoform assembly, quantitation </td> </tr> <tr> <td> <a href="myrna">Myrna</a>: Cloud, differential gene expression </td> </tr> <tr> <td> <a href="https://github.com/mourisl/Lighter">Lighter</a>: Fast error correction </td> </tr> <tr> <td> <a href="other_tools.shtml">Other tools using Bowtie</a> </td> </tr> </table> </ul> </div> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/"><h2><u>Pre-built indexes</u></h2></a> <div class="box"> <table width="100%"> <p style="font-size: small; line-height: 130%"> Consider using Illumina's <a href="http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn">iGenomes</a> collection. Each iGenomes archive contains pre-built Bowtie and <a href="bowtie2">Bowtie 2</a> indexes. <br/><br/> </p>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/GRCh38_no_alt.zip"><i>H. sapiens</i>, NCBI GRCh38</a> </td><td align="right"> <b>2.7 GB</b> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj_bt.zip"><i>H. sapiens</i>, NCBI GRCh38 <br/> with 1KGenomes major SNPs</a> </td><td align="right"> <b>2.7 GB</b> </td></tr> <tr><td colspan="2" style="font-size: x-small">  <a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj.fa.gz">FASTA</a> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip"><i>H. sapiens</i>, UCSC hg19</a> </td><td align="right"> <b>2.7 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_1kgmaj_bt.zip"><i>H. sapiens</i>, UCSC hg19 <br/> with 1KGenomes major SNPs</a> </td><td align="right"> <b>2.7 GB</b> </td></tr> <tr><td colspan="2" style="font-size: x-small">  <a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_1kgmaj.fa.gz">FASTA</a> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18.ebwt.zip"><i>H. sapiens</i>, UCSC hg18</a> </td><td align="right"> <b>2.7 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm.ebwt.zip"><i>H. sapiens</i>, NCBI v37</a> </td><td align="right"> <b>2.7 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm.ebwt.zip"><i>H. sapiens</i>, NCBI v36</a> </td><td align="right"> <b>2.7 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8.ebwt.zip"><i>M. musculus</i>, UCSC mm8</a> </td><td align="right"> <b>2.4 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9.ebwt.zip"><i>M. musculus</i>, UCSC mm9</a> </td><td align="right"> <b>2.4 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37.ebwt.zip"><i>M. musculus</i>, NCBI v37</a> </td><td align="right"> <b>2.4 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4.ebwt.zip"><i>R. norvegicus</i>, UCSC rn4</a> </td><td align="right"> <b>2.4 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus.ebwt.zip"><i>B. taurus</i>, UMD v3.0</a> </td><td align="right"> <b>2.4 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2.ebwt.zip"><i>C. familiaris</i>, UCSC canFam2</a> </td><td align="right"> <b>2.4 GB</b> </td></tr> <tr><td colspan=2><table width="100%">  <tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2_c.ebwt.zip">full</a>  </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/galGal3.ebwt.zip"><i>G. gallus</i>, UCSC, galGal3</a> </td><td align="right"> <b>1.1 GB</b> </td></tr> <tr><td colspan=2><table width="100%"><tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/galGal3_c.ebwt.zip">full</a> </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/d_melanogaster_fb5_22.ebwt.zip"><i>D. melanogaster</i>, Flybase, r5.22</a> </td><td align="right"> <b>150 MB</b> </td></tr> <tr><td colspan=2><table width="100%"><tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/d_melanogaster_fb5_22_c.ebwt.zip">full</a> </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/a_thaliana.ebwt.zip"><i>A. thaliana</i>, TAIR, TAIR9</a> </td><td align="right"> <b>120 MB</b> </td></tr> <tr><td colspan=2><table width="100%"><tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/a_thaliana_c.ebwt.zip">full</a> </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/c_elegans_ws200.ebwt.zip"><i>C. elegans</i>, Wormbase, WS200</a> </td><td align="right"> <b>75 MB</b> </td></tr> <tr><td colspan=2><table width="100%"><tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/c_elegans_ws200_c.ebwt.zip">full</a> </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/s_cerevisiae.ebwt.zip"><i>S. cerevisiae</i>, CYGD</a> </td><td align="right"> <b>15 MB</b> </td></tr> <tr><td colspan=2><table width="100%"><tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/s_cerevisiae_c.ebwt.zip">full</a> </tr></table> </td></tr>  <tr><td> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/e_coli.ebwt.zip"><i>E. coli</i>, NCBI, st. 536</a> </td><td align="right"> <b>5 MB</b> </td></tr> <tr><td colspan=2><table width="100%"><tr> <td> colorspace: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/e_coli_c.ebwt.zip">full</a> </tr></table> </td></tr> </table> <p style="font-size: x-small; line-height: 130%"> All indexes are for assemblies, not contigs. Unplaced or unlocalized sequences and alternate haplotype assemblies are excluded.</p> <p style="font-size: x-small; line-height: 130%"> Some unzip programs cannot handle archives >2 GB. If you have problems downloading or unzipping a >2 GB index, try downloading in two parts.</p> <p style="font-size: x-small; line-height: 130%">Check .zip file integrity with <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/md5sum.txt">MD5s</a>.</p> </div> <h2>Publications</h2> <div class="box"> <ul> <li style="font-size: x-small; line-height: 130%">Langmead B, Trapnell C, Pop M, Salzberg SL. <a href="http://genomebiology.com/2009/10/3/R25"><b>Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</b></a>. <i><a href="http://genomebiology.com">Genome Biology</a></i> <b>10</b>:R25. <br/><br/> <li style="font-size: x-small; line-height: 130%">Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. <a href="http://genomebiology.com/2009/10/11/R134"><b>Searching for SNPs with cloud computing</b></a>. <i><a href="http://genomebiology.com">Genome Biology</a></i> <b>10</b>:R134. <br/><br/> <li style="font-size: x-small; line-height: 130%">Trapnell C, Pachter L, Salzberg SL, <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp120"><b>TopHat: discovering splice junctions with RNA-Seq</b></a>. <i><a href="http://bioinformatics.oxfordjournals.org/">Bioinformatics</a></i> 2009 25(9):1105-1111.</li> </ul> </div>  <h2>Contributors</h2> <div class="box"> <ul> <li><a href="http://www.cs.jhu.edu/~langmea/index.shtml">Ben Langmead</a></li> <li><a href="http://www.broadinstitute.org/~cole/">Cole Trapnell</a></li> <li><a href="http://www.ccb.jhu.edu/people/infphilo">Daehwan Kim</a></li> <li>Rone Charles</li> <li>Chris Wilks</li> <li>Valentin Antonescu</li> </ul> </div> <h2>Related links</h2> <div class="box"> <ul> <li><a href="http://scholar.google.com/scholar?cites=9743535340779752835&as_sdt=20000005&sciodt=0,21&hl=en">Papers citing Bowtie</a></li> <li><a href="http://www.jhu.edu/">Johns Hopkins University</a></li> <li><a href="http://www.cs.jhu.edu/">JHU Computer Science</a></li> </ul> </div> </div>  <div id="leftside"> <h2>Tools that use Bowtie (or Bowtie 2):</h2> <ul> <li>mRNA sequencing:</li> <ul> <li><a href="myrna">Myrna</a> (<a href="http://genomebiology.com/2010/11/8/R83">paper</a>)</li> <li><a href="http://tophat.cbcb.umd.edu/">TopHat, TopHat 2</a> (<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp120">paper</a>)</li> <li><a href="http://cufflinks.cbcb.umd.edu/">Cufflinks</a> (<a href="http://dx.doi.org/10.1038/nbt.1621">paper</a>)</li> <li><a href="http://trinityrnaseq.sourceforge.net/">Trinity</a> (<a href="http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html">paper</a>)</li> <li><a href="http://www.netlab.uky.edu/p/bioinfo/MapSplice/">MapSplice</a> (<a href="http://nar.oxfordjournals.org/content/38/18/e178.full">paper</a>)</li> <li><a href="http://bioinformatics.mdanderson.org/main/SpliceSeq:Methods">SpliceSeq (<a href="http://bioinformatics.oxfordjournals.org/content/early/2012/07/20/bioinformatics.bts452.short">paper</a>)</a></li> <li><a href="https://github.com/rnaseqr/RNASEQR">RNASEQR</a> (<a href="http://nar.oxfordjournals.org/content/early/2011/12/22/nar.gkr1248.short">paper</a>)</li> <li><a href="http://deweylab.biostat.wisc.edu/rsem/">RSEM</a> (<a href="http://www.biomedcentral.com/1471-2105/12/323/">paper</a>)</li> <li><a href="http://changlab.cgrb.oregonstate.edu/node/26">GENE-counter</a> (<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025279">paper</a>)</li> <li><a href="http://mapman.gabipd.org/web/guest/robin">RobiNA</a> (<a href="http://nar.oxfordjournals.org/content/early/2012/06/08/nar.gks540">paper</a>)</li> <li><a href="http://blog.expressionplot.com/">ExpressionPlot</a> (<a href="http://genomebiology.com/2011/12/7/R69">paper</a>)</li> <li><a href="http://cbil.upenn.edu/RUM/">RUM</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/18/2518.long">paper</a>)</li> <li><a href="http://www.bio.anl.gov/molecular_and_systems_biology/bowstrap/bowstrap_download.html">BowStrap</a> (<a href="http://www.biomedcentral.com/1756-0500/5/275/abstract">paper</a>)</li> <li><a href="http://www.bio.ifi.lmu.de/softwareservices/contextmap">ContextMap</a> (<a href="http://www.biomedcentral.com/1471-2105/13/S6/S9">paper</a>)</li> <li><a href="http://bio.math.berkeley.edu/eXpress/overview.html">eXpress</a> (<a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2251.html">paper</a>)</li> <li><a href="http://bio.math.berkeley.edu/ReXpress/">ReXpress</a> (<a href="http://bioinformatics.oxfordjournals.org/content/early/2013/05/14/bioinformatics.btt197.short?rss=1">paper</a>)</li> <li><a href="http://bioen-compbio.bioen.illinois.edu/TrueSight/">TrueSight</a> (<a href="http://nar.oxfordjournals.org/content/early/2012/12/18/nar.gks1311.full.pdf">paper</a>)</li> <li><a href="http://genome.ufl.edu/rivalab/PASTA/">PASTA</a> (<a href="http://www.biomedcentral.com/content/pdf/1471-2105-14-116.pdf">paper</a>)</li> <li><a href="https://sites.google.com/site/qrnaseq/">QRNAseq</a></li> </ul> <li>Bisulfite-seq:</li> <ul> <li><a href="http://rafalab.jhsph.edu/bsmooth/">BSmooth</a> (<a href="http://genomebiology.com/2012/13/10/R83">paper</a>)</li> <li><a href="http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/">Bismark</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/11/1571.short">paper</a>)</li> <li><a href="https://github.com/brentp/methylcode">MethylCoder</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/17/2435.short">paper</a>)</li> <li><a href="http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html">BS-Seeker</a> (<a href="http://www.biomedcentral.com/1471-2105/11/203">paper</a>)</li> <li><a href="http://code.google.com/p/bsolana/">B-SOLANA</a> (<a href="http://bioinformatics.oxfordjournals.org/content/28/3/428.long">paper</a>)</li> <li><a href="http://sing.ei.uvigo.es/bicycle/">Bicycle</a></li> <li><a href="http://sourceforge.net/projects/dna-bison/">Bison</a></li> </ul> <li>Re-seqeuncing:</li> <ul> <li><a href="crossbow">Crossbow</a> (<a href="http://genomebiology.com/2009/10/11/R134">paper</a>)</li> </ul> <li>Assembly and scaffolding:</li> <ul> <li><a href="http://lge.ibi.unicamp.br/zorro/">Zorro</a></li> <li><a href="http://www.baseclear.com/landingpages/sspacev12/">SSPACE</a> (<a href="http://bioinformatics.oxfordjournals.org/content/early/2010/12/12/bioinformatics.btq683.short">paper</a>)</li> <li><a href="http://impact.crhc.illinois.edu">TIGER</a> (<a href="http://www.biomedcentral.com/1471-2105/13/S19/S18">paper</a>)</li> </ul> <li>Workflow:</li> <ul> <li><a href="http://main.g2.bx.psu.edu/">Galaxy</a> (<a href="http://genomebiology.com/2010/11/8/R86">paper</a>)</li> <li><a href="http://chipster.csc.fi/">Chipster</a> (<a href="http://www.biomedcentral.com/1471-2164/12/507/abstract/">paper</a>)</li> <li><a href="http://www.lgtc.nl/services/general_services/software_tools/gapss.php">GAPSS</a></li> <li><a href="http://ugene.unipro.ru/">Unipro UGENE</a> (<a href="http://bioinformatics.oxfordjournals.org/content/28/8/1166.full">paper</a>)</li> <li><a href="http://code.google.com/p/biopieces/">Biopieces</a></li> <li><a href="https://insilico.ulb.ac.be/">InSilico DB</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/22/3204">paper</a>)</li> <li><a href="http://pipeline.loni.ucla.edu">LONI Pipeline</a> (<a href="http://www.biomedcentral.com/1471-2105/12/304">paper</a>)</li> <li><a href="http://kbase.us/for-users/user-home/">KBase</a></li> <li><a href="http://biokepler.org/bioactor_docs">bioKepler</a></li> </ul> <li>Structural variants:</li> <ul> <li><a href="http://sourceforge.net/apps/mediawiki/n-fuse/index.php?title=NFuse_0.0.1">nFuse</a> (<a href="http://genome.cshlp.org/content/early/2012/10/04/gr.136572.111">paper</a>)</li> </ul> <li>Gene fusion:</li> <ul> <li><a href="http://tophat.cbcb.umd.edu/fusion_index.html">TopHat Fusion</a> (<a href="http://genomebiology.com/2011/12/8/R72/abstract">paper</a>)</li> <li><a href="http://compbio.bccrc.ca/software/defuse">deFuse</a> (<a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138">paper</a>)</li> <li><a href="http://code.google.com/p/comrad/">Comrad</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/11/1481.abstract">paper</a>)</li> <li><a href="https://bitbucket.org/mckinsel/shortfuse">ShortFuse</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/8/1068.full.pdf">paper</a>)</li> <li><a href="http://bioen-compbio.bioen.illinois.edu/FusionHunter/">FusionHunter</a> (<a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/05/bioinformatics.btr265.abstract">paper</a>)</li> <li><a href="http://mayoresearch.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm">SnowShoes-FD</a> (<a href="http://nar.oxfordjournals.org/content/early/2011/05/27/nar.gkr362.full">paper</a>)</li> <li><a href="http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/">FusionFinder</a> (<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039987">paper</a>)</li> <li><a href="http://code.google.com/p/chimerascan/">Chimerascan</a> (<a href="http://bioinformatics.oxfordjournals.org/content/27/20/2903.long">paper</a>)</li> <li><a href="https://sites.google.com/site/fusionq1/home/">FusionQ</a> (<a href="http://www.biomedcentral.com/1471-2105/14/193/abstract">paper</a>)</li> </ul> <li>Metagenomics:</li> <ul> <li><a href="http://genomics1.mh-hannover.de/genometa/index.php?Site=Tutorial%201">Genometa</a> (<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0041224">paper</a>)</li> <li><a href="http://huttenhower.sph.harvard.edu/metaphlan">MetaPhlan</a> (<a href="http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2066.html">paper</a>)</li> <li><a href="http://blog.metagenomics.anl.gov/howto/quality-control/">MG-RAST</a> (<a href="http://blog.metagenomics.anl.gov/howto/quality-control/">paper</a>)</li> <li><a href="https://github.com/treangen/metAMOS/wiki">metAMOS</a> (<a href="http://genomebiology.com/2013/14/1/R2/abstract">paper</a>)</li> </ul> <li>Small RNA:</li> <ul> <li><a href="http://www.ufrgs.br/RNAi/isomiRID/">isomiRID</a> (<a href="http://bioinformatics.oxfordjournals.org/content/29/20/2521.full">paper</a>) <li><a href="http://deqor.mpi-cbg.de/deqor_new/input.html">Deqor v3</a> (<a href="http://nar.oxfordjournals.org/content/32/suppl_2/W113.full">paper</a>) <li><a href="http://b110-wiki.dkfz.de/signaling/wiki/display/nextrnai/NEXT-RNAi">NEXT-RNAi</a> (design of genome-wide RNAi libraries)</li> <li><a href="http://evolution.sysu.edu.cn/software/mirevo.htm">miREvo</a> (<a href="http://www.biomedcentral.com/1471-2105/13/140">paper</a>)</li> <li><a href="http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php">miRanalyzer</a> (<a href="http://nar.oxfordjournals.org/content/39/suppl_2/W132.full">paper</a>)</li> <li><a href="http://www.ebi.ac.uk/enright-srv/MapMi/">MapMi</a> (<a href="http://www.biomedcentral.com/1471-2105/11/133">paper</a>)</li> <li><a href="http://users-mb.au.dk/pmgrp/shortran/">shortran</a> (<a href="http://bioinformatics.oxfordjournals.org/content/early/2012/08/22/bioinformatics.bts496.full.pdf+html">paper</a>)</li> <li><a href="http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html">miRDeep2</a> (<a href="http://nar.oxfordjournals.org/content/40/1/37.full">paper</a>)</li> <li><a href="http://ngs.ym.edu.tw/ym500/">YM500</a> (<a href="http://nar.oxfordjournals.org/content/41/D1/D285.full">paper</a>)</li> <li><a href="http://starbase.sysu.edu.cn">starBase</a> (<a href="http://nar.oxfordjournals.org/content/39/suppl_1/D202.full">paper</a>)</li> </ul> <li>Other:</li> <ul> <li><a href="http://ab.inf.uni-tuebingen.de/software/pauda/">PADUA</a> (alignment of DNA to protein databases; <a href="http://bioinformatics.oxfordjournals.org/content/early/2013/05/07/bioinformatics.btt254.full.pdf+html">paper</a>) <li><a href="http://personalpages.manchester.ac.uk/staff/antonio.marco/seqtrimmap.html">SeqTrimMap</a> (sequential trimming and mapping; <a href="http://bioinformatics.oxfordjournals.org/content/28/3/318.full">paper</a>) <li><a href="http://www.mcardle.wisc.edu/mprime/version.html">mPrime</a> (primer design)</li> <li><a href="https://github.com/csmiller/EMIRGE">EMIGRE</a> (ribosomal genes reconstruction; <a href="http://genomebiology.com/2011/12/5/R44">paper</a>)</li> <li><a href="http://sourceforge.net/p/tapdancebio/home/Home/">TAPDANCE</a> (identifies CISs in transposon junction fragment insertion data; <a href="http://www.biomedcentral.com/content/pdf/1471-2105-13-154.pdf">paper</a>)</li> <li><a href="http://carla.saleh.free.fr/software/paparazzi.html">Paparazzi</a> (reconstruction of viral genomes from small RNA reads; <a href="http://jvi.asm.org/content/85/21/11016.long">paper</a>)</li> <li><a href="https://github.com/capsid/capsid">CaPSID</a> (pathogen detection; <a href="http://www.biomedcentral.com/1471-2105/13/206">paper</a>) <li><a href="http://eupathdb.org/eupathdb/">EuPathDB</a> (eukaryotic pathogen detection; <a href="http://nar.oxfordjournals.org/content/41/D1/D684.full">paper</a>) </ul> </ul> <h2>OS distributions with Bowtie packages</h2> <ul> <li><a href="http://packages.ubuntu.com/search?suite=default&section=all&arch=any&searchon=names&keywords=bowtie">Ubuntu</a></li> <li><a href="http://packages.debian.org/search?searchon=names&keywords=bowtie">Debian</a></li> <li><a href="https://apps.fedoraproject.org/packages/bowtie">Fedora</a></li> <li><a href="http://www.macports.org/ports.php?by=name&substr=bowtie">MacPorts</a></li> </ul> <h2>Commercial products using Bowtie:</h2> <ul> <li><a href="http://www.geospiza.com/Products/WhitePaper_06102009.pdf">Geospiza GeneSifter</a></li> <li><a href="http://www.clcbio.com/index.php?id=1408&manual=External_applications_integration_Bowtie.html">CLC Genomics Server</a></li> <li><a href="http://www.partek.com/flow">Partek Flow</a></li> <li><a href="https://igor.sbgenomics.com/lab/public/pipelines/">SevenBridges genomics</a></li> <li><a href="http://www.appistry.com/products/ngs-pipelines/bioinformatics-pipeline-suite">Appistry</a></li> <li><a href="http://www.maverixbio.com/opensource/">Maverix Biomics</a></li> </ul> <h2>Published protocols using Bowtie 1 and/or 2:</h2> <ul> <li>Wang S, et al. <a href="http://www.nature.com/nprot/journal/v8/n12/full/nprot.2013.150.html">Target analysis by integration of transcriptome and ChIP-seq data with BETA</a>. <i>Nature Protocols</i>.</li> <li>Hisano M, et al. <a href="http://www.nature.com/nprot/journal/v8/n12/full/nprot.2013.145.html">Genome-wide chromatin analysis in mature mouse and human spermatozoa</a>. <i>Nature Protocols</i>.</li> <li>Becker AH, et al. <a href="http://www.nature.com/nprot/journal/v8/n11/full/nprot.2013.133.html">Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes</a>. <i>Nature Protocols</i>.</li> <li>Anders S, et al. <a href="http://www.nature.com/nprot/journal/v8/n9/full/nprot.2013.099.html">Count-based differential expression analysis of RNA sequencing data using R and Bioconductor</a>. <i>Nature Protocols</i>.</li> <li>Wan Y, et al. <a href="http://www.nature.com/nprot/journal/v8/n5/full/nprot.2013.045.html">Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing</a>. <i>Nature Protocols</i>.</li> <li>Haas BJ, et al. <a href="http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html">De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis</a>. <i>Nature Protocols</i>.</li> <li>Ingolia NT, et al. <a href="http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb0418s103/full"> Genome-Wide Annotation and Quantitation of Translation by Ribosome Profiling</a>. <i>Current Protocols in Molecular Biology</i>.</li> <li>Baslan T, et al. <a href="http://www.nature.com/nprot/journal/v7/n6/abs/nprot.2012.039.html"> Genome-wide copy number analysis of single cells</a>. <i>Nature Protocols</i>.</li> <li>Trapnell C, et al. <a href="http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html"> Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks</a>. <i>Nature Protocols</i>.</li> <li>Ingolia NT, et al. <a href="http://www.nature.com/nprot/journal/v7/n8/full/nprot.2012.086.html"> The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments</a>. <i>Nature Protocols</i>.</li> <li>Bardet AF, et al. <a href="http://www.nature.com/nprot/journal/v7/n1/full/nprot.2011.420.html"> A computational pipeline for comparative ChIP-seq analyses</a>. <i>Nature Protocols</i>.</li> <li>Simon JS, et al. <a href="http://www.nature.com/nprot/journal/v7/n2/full/nprot.2011.444.html"> Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA</a>. <i>Nature Protocols</i>.</li> <li>Goodman AL, et al. <a href="http://www.nature.com/nprot/journal/v6/n12/full/nprot.2011.417.html">Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries</a>. <i>Nature Protocols</i>.</li> <li>Fanelli M, et al. <a href="http://www.nature.com/nprot/journal/v6/n12/full/nprot.2011.406.html">Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue</a>. <i>Nature Protocols</i>.</li> <li>Christodoulou DC, et al.<a href="http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb25b09s93/full">Quantification of Gene Transcripts with Deep Sequencing Analysis of Gene Expression (DSAGE) Using 1 to 2 micrograms Total RNA</a>. <i>Current Protocols in Molecular Biology</i>.</li> </a></li> </ul> </div> </div> <div id="footer"> <table width="100%" cellspacing=15><tr><td> This research was supported in part by NIH grants R01-LM006845, R01-GM083873 and P41HG004059. </td></tr> </table> <center><a href="http://www.sourceforge.net"><img src="./images/sflogo.png" alt="Sourceforge.net" style="border-style: none"></img></a></center> </div> </div>  <script type="text/javascript"> var gaJsHost = (("https:" == document.location.protocol) ? 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