hisat-3n/docs_jhu/sidebar.inc.shtml

<h2>Site Map</h2>
<div class="box">
 <ul>
   <li><a href="index.shtml">Home</a></li>
   <li><a href="manual.shtml">Manual</a></li>
   <li><a href="faq.shtml">FAQ</a></li>
 </ul>
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<h2>News and Updates</h2>
<div class="box">
 <ul>
   <table width="100%">
	 <tbody><tr><td>New releases and related tools will be announced through the Bowtie
     <a href="https://lists.sourceforge.net/lists/listinfo/bowtie-bio-announce"><b>mailing list</b></a>.</td></tr>
   </tbody></table>
 </ul>
</div>

<h2>Getting Help</h2>
<div class="box">
 <ul>
   <table width="100%">
     <tbody><tr><td>
	   <!-- 
		Questions and comments about HISAT2 can be posted on the 
		<a href="https://groups.google.com/forum/#!forum/hisat-tools-users"><b>HISAT2 Tools Users Google Group</b></a>.
		-->
		Please use <a href="mailto:hisat2.genomics@gmail.com">hisat2.genomics@gmail.com</a> for 
		private communications only. Please do not email technical questions to HISAT2 contributors directly.</td></tr>
   </tbody></table>
 </ul>
</div>

<a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads"><h2><u>Releases</u></h2></a>
<div class="box">
 <ul>
   <table width="100%"><tbody><tr><td>version 2.1.0</td> <td align="right">6/8/2017</td></tr>
       <tr>
	 <td><a href="https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-source/download" onclick="javascript: pageTracker._trackPageview('/downloads/hisat'); ">&nbsp;&nbsp;&nbsp;Source code</a></td>
       </tr>
       <tr>
	 <td><a href="https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-Linux_x86_64/download" onclick="javascript: pageTracker._trackPageview('/downloads/hisat'); ">&nbsp;&nbsp;&nbsp;Linux x86_64 binary</a></td>
       </tr>
       <tr>
	 <td><a href="https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-OSX_x86_64/download" onclick="javascript: pageTracker._trackPageview('/downloads/hisat'); ">&nbsp;&nbsp;&nbsp;Mac OS X x86_64 binary</a></td>
       </tr>
       <tr>
	 <td><a href="http://www.di.fc.ul.pt/~afalcao/hisat2_windows.html" onclick="javascript: pageTracker._trackPageview('/downloads/hisat'); ">&nbsp;&nbsp;&nbsp;Windowns binary</a></td>
       </tr>
   </tbody></table>
 </ul>
<font size="-1">Please cite: <p>Kim D, Langmead B and Salzberg SL. <a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3317.html"><b>HISAT: a fast spliced aligner with low memory requirements</b></a>. <i><a href="http://www.nature.com/nmeth">Nature Methods</a></i></font> 2015</p>
</div>

<h2><a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data"><u>Indexes</u></a> (see <a href="indexes.txt"><u>note</u><a>)</h2>
  <div class="box">
    <table width="100%">
      <tr>
      <td colspan="2">
         <i>H. sapiens</i>, GRCh38
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch38/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.9 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch38_snp/download"><i>genome_snp</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.6 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch38_tran/download"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.1 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch38_snp_tran/download"><i>genome_snp_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.6 GB</b>
        </td>
      </tr>
      
      <tr>
	<td colspan="2">
          <i>H. sapiens</i>, UCSC hg38
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/hg38/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.1 GB</b>
        </td>
      </tr>

      <tr>
	<td colspan="2">
          <i>H. sapiens</i>, UCSC hg38 and Refseq gene annotations referred to in <a href="">the Nature Protocol paper</a>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/hg38_tran/download"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.2 GB</b>
        </td>
      </tr>

      <tr>
        <td colspan="2">
         <i>H. sapiens</i>, GRCh37
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch37/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.9 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch37_snp/download"><i>genome_snp</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.5 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch37_tran/download"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.0 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grch37_snp_tran/download"><i>genome_snp_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.5 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2">
          <i>H. sapiens</i>, UCSC hg19
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/hg19/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.9 GB</b>
        </td>
      </tr>

      <tr>
      <td colspan="2">
         <i>M. musculus</i>, GRCm38
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grcm38/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.7 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grcm38_snp/download"><i>genome_snp</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.0 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.7 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/grcm38_snp_tran/download"><i>genome_snp_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>4.0 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2">
          <i>M. musculus</i>, UCSC mm10
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/mm10/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.5 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2">
          <i>R. norvegicus</i>, UCSC rn6
        </td>
      </tr>
      <tr>
        <td>
	  <a href="https://cloud.biohpc.swmed.edu/index.php/s/rn6/download"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>3.7 GB</b>
        </td>
      </tr>
      <tr>
      <td colspan="2">
         <i>D. melanogaster</i>, BDGP6
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/bdgp6.tar.gz"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.2 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/bdgp6_tran.tar.gz"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.2 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2">
          <i>D. melanogaster</i>, UCSC dm6
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/dm6.tar.gz"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.2 GB</b>
        </td>
      </tr>
      
      <tr>
      <td colspan="2">
         <i>C. elegans</i>, WBcel235
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/wbcel235.tar.gz"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.1 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/wbcel235_tran.tar.gz"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.1 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2">
          <i>C. elegans</i>, UCSC ce10
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/ce10.tar.gz"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.1 GB</b>
        </td>
      </tr>
      
      <tr>
      <td colspan="2">
         <i>S. cerevisiae</i>, R64-1-1
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/r64.tar.gz"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.01 GB</b>
        </td>
      </tr>
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/r64_tran.tar.gz"><i>genome_tran</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.01 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2">
          <i>S. cerevisiae</i>, UCSC sacCer3
        </td>
      </tr>      
      <tr>
        <td>
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/sc3.tar.gz"><i>genome</i></a>
        </td>
	<td align="right" style="font-size: x-small">
	  <b>0.01 GB</b>
        </td>
      </tr>
      <tr>
	<td colspan="2" style="font-size: x-small">
	  <br/>
	  * <i>genome</i>: HFM index for reference
        </td>
      </tr>
      <tr>
	<td colspan="2" style="font-size: x-small">
	  * <i>genome_snp</i>: HGFM index for reference plus SNPs
        </td>
      </tr>
      <tr>
	<td colspan="2" style="font-size: x-small">
	  * <i>genome_tran</i>: HGFM index for reference plus transcripts
        </td>
      </tr>
      <tr>
	<td colspan="2" style="font-size: x-small">
	  * <i>genome_snp_tran</i>: HGFM index for reference plus SNPs and transcripts
        </td>
      </tr>
      <tr>
	<td colspan="2" style="font-size: x-small">
	  <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data">more indexes</a>
        </td>
      </tr>
    </table>
  </div>

<h2>Related Tools</h2>
<div class="box">
  <ul>
    <li><a href="http://www.ccb.jhu.edu/hisat-genotype">HISAT-genotype</a>: Next-generation analysis of human genomes</li>
   <li><a href="http://www.ccb.jhu.edu/software/hisat">HISAT</a>: Fast and sensitive spliced alignment</li>
   <li><a href="http://bowtie-bio.sourceforge.net/bowtie2">Bowtie2</a>: Ultrafast read alignment</li>
   <li><a href="http://www.ccb.jhu.edu/software/tophat">TopHat2</a>: Spliced read mapper for RNA-Seq</li>
   <li><a href="http://cufflinks.cbcb.umd.edu">Cufflinks</a>: Isoform assembly and quantitation for RNA-Seq</li>
   <li><a href="http://www.ccb.jhu.edu/software/stringtie">StringTie</a>: Transcript assembly and quantification for RNA-Seq</li>
 </ul>
</div>

<h2>Publications</h2>
<div class="box">
 <ul>
   <li><p>Kim D, Langmead B and Salzberg SL. <a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3317.html"><b>HISAT: a fast spliced aligner with low memory requirements</b></a>. <i><a href="http://www.nature.com/nmeth">Nature Methods</a></i> 2015</p></li>
   <li><p>Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. <a href="http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html"><b>Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown</b></a>. <i><a href="http://www.nature.com/nprot">Nature Protocols</a></i> 2016</p></li>
 </ul>
</div>

<h2>Contributors</h2>
<div class="box">
 <ul>
   <li><a href="http://kim-lab.org">Daehwan Kim</a></li>
   <li><a href="http://www.cs.jhu.edu/~langmea">Ben Langmead</a></li>
   <li><a href="">Joe Paggi</a></li>
   <li>Geo Pertea</li>
   <li><a href="http://salzberg-lab.org/about-me/">Steven Salzberg</a></li>
 </ul>
</div>

<h2>Links</h2>
<div class="box">
 <ul>
   <li><a href="http://www.ccb.jhu.edu/">Center for Computational Biology at Johns Hopkins University </a></li>
   <li><a href="http://www.cs.jhu.edu/">Computer Science Department at Johns Hopkins University </a></li>
 </ul>
</div>