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<div class="section" id="htseq-analysing-high-throughput-sequencing-data-with-python">
<span id="overview"></span><h1>HTSeq: Analysing high-throughput sequencing data with Python<a class="headerlink" href="#htseq-analysing-high-throughput-sequencing-data-with-python" title="Permalink to this headline">¶</a></h1>
<p>HTSeq is a Python package that provides infrastructure to process data
from high-throughput sequencing assays.</p>
<ul class="simple">
<li>Please see the chapter <a class="reference internal" href="tour.html#tour"><span class="std std-ref">A tour through HTSeq</span></a> first for an overview on the kind of analysis
you can do with HTSeq and the design of the package, and then look at the reference
documentation.</li>
</ul>
<ul class="simple">
<li>While the main purpose of HTSeq is to allow you to write your own analysis scripts,
customized to your needs, there are also a couple of stand-alone scripts for
common tasks that can be used without any Python knowledge. See the <em>Scripts</em>
section in the overview below for what is available.</li>
</ul>
<ul class="simple">
<li>For downloads and installation instructions, see <a class="reference internal" href="install.html#install"><span class="std std-ref">Prequisites and installation</span></a>.</li>
</ul>
<div class="section" id="paper">
<h2>Paper<a class="headerlink" href="#paper" title="Permalink to this headline">¶</a></h2>
<p>HTSeq is described in the following publication (which is currently under review but already
available as preprint):</p>
<blockquote>
<div><div class="line-block">
<div class="line">Simon Anders, Paul Theodor Pyl, Wolfgang Huber</div>
<div class="line"><em>HTSeq — A Python framework to work with high-throughput sequencing data</em></div>
<div class="line">bioRxiv preprint (2014), <a class="reference external" href="http://dx.doi.org/10.1101/002824">doi: 10.1101/002824</a></div>
</div>
</div></blockquote>
<p>If you use HTSeq in research, please cite this paper in your publication.</p>
</div>
<div class="section" id="documentation-overview">
<h2>Documentation overview<a class="headerlink" href="#documentation-overview" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first"><a class="reference internal" href="install.html#install"><span class="std std-ref">Prequisites and installation</span></a></p>
<p>Download links and installation instructions can be found here</p>
</li>
<li><p class="first"><a class="reference internal" href="tour.html#tour"><span class="std std-ref">A tour through HTSeq</span></a></p>
<p>The Tour shows you how to get started. It explains how to install HTSeq, and then
demonstrates typical analysis steps with explicit examples. Read this first, and
then see the Reference for details.</p>
</li>
<li><p class="first"><a class="reference internal" href="tss.html#tss"><span class="std std-ref">A detailed use case: TSS plots</span></a></p>
<p>This chapter explains typical usage patterns for HTSeq by explaining in detail
three different solutions to the same programming task.</p>
</li>
<li><p class="first">Reference documentation</p>
<p>The various classes of <cite>HTSeq</cite> are described here.</p>
<ul>
<li><p class="first"><a class="reference internal" href="sequences.html#sequences"><span class="std std-ref">Sequences and FASTA/FASTQ files</span></a></p>
<p>In order to represent sequences and reads (i.e., sequences with base-call quality
information), the classes <a class="reference internal" href="sequences.html#HTSeq.Sequence" title="HTSeq.Sequence"><code class="xref py py-class docutils literal"><span class="pre">Sequence</span></code></a> and <a class="reference internal" href="sequences.html#HTSeq.SequenceWithQualities" title="HTSeq.SequenceWithQualities"><code class="xref py py-class docutils literal"><span class="pre">SequenceWithQualities</span></code></a> are used.
The classes <a class="reference internal" href="sequences.html#HTSeq.FastaReader" title="HTSeq.FastaReader"><code class="xref py py-class docutils literal"><span class="pre">FastaReader</span></code></a> and <a class="reference internal" href="sequences.html#HTSeq.FastqReader" title="HTSeq.FastqReader"><code class="xref py py-class docutils literal"><span class="pre">FastqReader</span></code></a> allow to parse FASTA and FASTQ
files.</p>
</li>
<li><p class="first"><a class="reference internal" href="genomic.html#genomic"><span class="std std-ref">Genomic intervals and genomic arrays</span></a></p>
<p>The classes <a class="reference internal" href="genomic.html#HTSeq.GenomicInterval" title="HTSeq.GenomicInterval"><code class="xref py py-class docutils literal"><span class="pre">GenomicInterval</span></code></a> and <a class="reference internal" href="genomic.html#HTSeq.GenomicPosition" title="HTSeq.GenomicPosition"><code class="xref py py-class docutils literal"><span class="pre">GenomicPosition</span></code></a> represent intervals and
positions in a genome. The class <a class="reference internal" href="genomic.html#HTSeq.GenomicArray" title="HTSeq.GenomicArray"><code class="xref py py-class docutils literal"><span class="pre">GenomicArray</span></code></a> is an all-purpose container
with easy access via a genomic interval or position, and <a class="reference internal" href="genomic.html#HTSeq.GenomicArrayOfSets" title="HTSeq.GenomicArrayOfSets"><code class="xref py py-class docutils literal"><span class="pre">GenomicArrayOfSets</span></code></a>
is a special case useful to deal with genomic features (such as genes, exons,
etc.)</p>
</li>
<li><p class="first"><a class="reference internal" href="alignments.html#alignments"><span class="std std-ref">Read alignments</span></a></p>
<p>To process the output from short read aligners in various formats (e.g., SAM),
the classes described here are used, to represent output files and alignments,
i.e., reads with their alignment information.</p>
</li>
<li><p class="first"><a class="reference internal" href="features.html#features"><span class="std std-ref">Features</span></a></p>
<p>The classes <a class="reference internal" href="features.html#HTSeq.GenomicFeature" title="HTSeq.GenomicFeature"><code class="xref py py-class docutils literal"><span class="pre">GenomicFeature</span></code></a> and <a class="reference internal" href="features.html#HTSeq.GFF_Reader" title="HTSeq.GFF_Reader"><code class="xref py py-class docutils literal"><span class="pre">GFF_Reader</span></code></a> help to deal with genomic
annotation data.</p>
</li>
<li><p class="first"><a class="reference internal" href="otherparsers.html#otherparsers"><span class="std std-ref">Other parsers</span></a></p>
<p>This page describes classes to parse VCF, Wiggle and BED files.</p>
</li>
<li><p class="first"><a class="reference internal" href="misc.html#misc"><span class="std std-ref">Miscellaneous</span></a></p>
</li>
</ul>
</li>
<li><p class="first">Scripts</p>
<p>The following scripts can be used without any Python knowledge.</p>
<ul>
<li><p class="first"><a class="reference internal" href="qa.html#qa"><span class="std std-ref">Quality Assessment with htseq-qa</span></a></p>
<p>Given a FASTQ or SAM file, this script produces a PDF file with plots depicting
the base calls and base-call qualities by position in the read. This is useful to
assess the technical quality of a sequencing run.</p>
</li>
<li><p class="first"><a class="reference internal" href="count.html#count"><span class="std std-ref">Counting reads in features with htseq-count</span></a></p>
<p>Given a SAM file with alignments and a GFF file with genomic features, this script
counts how many reads map to each feature.</p>
</li>
</ul>
</li>
<li><p class="first">Appendices</p>
</li>
</ul>
<blockquote>
<div><ul class="simple">
<li><a class="reference internal" href="history.html#history"><span class="std std-ref">Version history</span></a></li>
</ul>
</div></blockquote>
<blockquote>
<div><ul class="simple">
<li><a class="reference internal" href="contrib.html#contrib"><span class="std std-ref">Notes for Contributers</span></a></li>
</ul>
</div></blockquote>
<blockquote>
<div><ul class="simple">
<li><a class="reference internal" href="index.html#tableofcontents"><span class="std std-ref">Table of Contents</span></a></li>
</ul>
</div></blockquote>
<blockquote>
<div><ul class="simple">
<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
</ul>
</div></blockquote>
</div>
<div class="section" id="author">
<h2>Author<a class="headerlink" href="#author" title="Permalink to this headline">¶</a></h2>
<p>HTSeq is developed by <a class="reference external" href="http://www.embl.de/research/units/genome_biology/huber/members/index.php?s_personId=6001">Simon Anders</a> at <a class="reference external" href="http://www.embl.de/">EMBL Heidelberg</a> (<a class="reference external" href="http://www.embl.de/research/units/genome_biology/index.html">Genome Biology
Unit</a>). Please do not hesitate to contact me (anders <em>at</em> embl <em>dot</em> de) if you
have any comments or questions.</p>
</div>
<div class="section" id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h2>
<p>HTSeq is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.</p>
<p>This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.</p>
<p>The full text of the GNU General Public License, version 3, can be found
here: <a class="reference external" href="http://www.gnu.org/licenses/gpl-3.0-standalone.html">http://www.gnu.org/licenses/gpl-3.0-standalone.html</a></p>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">HTSeq: Analysing high-throughput sequencing data with Python</a><ul>
<li><a class="reference internal" href="#paper">Paper</a></li>
<li><a class="reference internal" href="#documentation-overview">Documentation overview</a></li>
<li><a class="reference internal" href="#author">Author</a></li>
<li><a class="reference internal" href="#license">License</a></li>
</ul>
</li>
</ul>
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