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<li><a class="reference internal" href="#">8. File formats</a><ul>
<li><a class="reference internal" href="#input-data-formats">8.1. Input data formats</a><ul>
<li><a class="reference internal" href="#newick-trees">Newick trees</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#specification">Specification</a></li>
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<li><a class="reference internal" href="#nhx-trees">NHX trees</a><ul>
<li><a class="reference internal" href="#id1">Introduction</a></li>
<li><a class="reference internal" href="#id2">Specification</a></li>
<li><a class="reference internal" href="#example">Example</a></li>
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<li><a class="reference internal" href="#sequences">Sequences</a></li>
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<li><a class="reference internal" href="#assignments">8.2. Assignments</a><ul>
<li><a class="reference internal" href="#read-assignments-in-sam-bam">Read assignments in SAM/BAM</a><ul>
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<li><a class="reference internal" href="#id5">Introduction</a></li>
<li><a class="reference internal" href="#id6">Specification</a></li>
<li><a class="reference internal" href="#id7">Examples</a></li>
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<li><a class="reference internal" href="#abundances-in-the-kraken-report-format">Abundances in the Kraken report format</a><ul>
<li><a class="reference internal" href="#id8">Introduction</a></li>
<li><a class="reference internal" href="#id9">Specification</a></li>
</ul>
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<li><a class="reference internal" href="#abundances-in-the-metaphlan2-report-format">Abundances in the MetaPhlAn2 report format</a><ul>
<li><a class="reference internal" href="#id10">Introduction</a></li>
<li><a class="reference internal" href="#id11">Specification</a></li>
</ul>
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<li><a class="reference internal" href="#abundances-in-the-centrifuge-report-format">Abundances in the Centrifuge report format</a><ul>
<li><a class="reference internal" href="#id12">Introduction</a></li>
<li><a class="reference internal" href="#id13">Specification</a></li>
<li><a class="reference internal" href="#id14">Example</a></li>
</ul>
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<li><a class="reference internal" href="#internal-prophyle-formats">8.4. Internal ProPhyle formats</a><ul>
<li><a class="reference internal" href="#index-6">ProPhyle Index</a><ul>
<li><a class="reference internal" href="#id16">Introduction</a></li>
<li><a class="reference internal" href="#id17">Specification</a></li>
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<section id="file-formats">
<span id="formats"></span><h1><span class="section-number">8. </span>File formats<a class="headerlink" href="#file-formats" title="Link to this heading">¶</a></h1>
<nav class="contents local" id="contents">
<ul class="simple">
<li><p><a class="reference internal" href="#input-data-formats" id="id30">Input data formats</a></p>
<ul>
<li><p><a class="reference internal" href="#newick-trees" id="id31">Newick trees</a></p>
<ul>
<li><p><a class="reference internal" href="#introduction" id="id32">Introduction</a></p></li>
<li><p><a class="reference internal" href="#specification" id="id33">Specification</a></p></li>
<li><p><a class="reference internal" href="#examples" id="id34">Examples</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#nhx-trees" id="id35">NHX trees</a></p>
<ul>
<li><p><a class="reference internal" href="#id1" id="id36">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id2" id="id37">Specification</a></p></li>
<li><p><a class="reference internal" href="#example" id="id38">Example</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#sequences" id="id39">Sequences</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#assignments" id="id40">Assignments</a></p>
<ul>
<li><p><a class="reference internal" href="#read-assignments-in-sam-bam" id="id41">Read assignments in SAM/BAM</a></p>
<ul>
<li><p><a class="reference internal" href="#id3" id="id42">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id4" id="id43">Specification</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#read-assignments-in-a-kraken-like-format" id="id44">Read assignments in a Kraken-like format</a></p>
<ul>
<li><p><a class="reference internal" href="#id5" id="id45">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id6" id="id46">Specification</a></p></li>
<li><p><a class="reference internal" href="#id7" id="id47">Examples</a></p></li>
</ul>
</li>
</ul>
</li>
<li><p><a class="reference internal" href="#abundances-estimates-experimental" id="id48">Abundances estimates (experimental)</a></p>
<ul>
<li><p><a class="reference internal" href="#abundances-in-the-kraken-report-format" id="id49">Abundances in the Kraken report format</a></p>
<ul>
<li><p><a class="reference internal" href="#id8" id="id50">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id9" id="id51">Specification</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#abundances-in-the-metaphlan2-report-format" id="id52">Abundances in the MetaPhlAn2 report format</a></p>
<ul>
<li><p><a class="reference internal" href="#id10" id="id53">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id11" id="id54">Specification</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#abundances-in-the-centrifuge-report-format" id="id55">Abundances in the Centrifuge report format</a></p>
<ul>
<li><p><a class="reference internal" href="#id12" id="id56">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id13" id="id57">Specification</a></p></li>
<li><p><a class="reference internal" href="#id14" id="id58">Example</a></p></li>
</ul>
</li>
</ul>
</li>
<li><p><a class="reference internal" href="#internal-prophyle-formats" id="id59">Internal ProPhyle formats</a></p>
<ul>
<li><p><a class="reference internal" href="#index-6" id="id60">ProPhyle Index</a></p>
<ul>
<li><p><a class="reference internal" href="#id16" id="id61">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id17" id="id62">Specification</a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#compressed-prophyle-index-for-transmission" id="id63">Compressed ProPhyle index for transmission</a></p>
<ul>
<li><p><a class="reference internal" href="#id18" id="id64">Introduction</a></p></li>
<li><p><a class="reference internal" href="#id19" id="id65">Specification</a></p></li>
</ul>
</li>
</ul>
</li>
</ul>
</nav>
<section id="input-data-formats">
<h2><span class="section-number">8.1. </span>Input data formats<a class="headerlink" href="#input-data-formats" title="Link to this heading">¶</a></h2>
<p>Node names should not contain the <code class="docutils literal notranslate"><span class="pre">@</span></code> character, and they should not be equal to <code class="docutils literal notranslate"><span class="pre">A</span></code>, <code class="docutils literal notranslate"><span class="pre">0</span></code>, and <code class="docutils literal notranslate"><span class="pre">root</span></code> (reserved names).</p>
<section id="newick-trees">
<span id="index-0"></span><h3>Newick trees<a class="headerlink" href="#newick-trees" title="Link to this heading">¶</a></h3>
<section id="introduction">
<h4>Introduction<a class="headerlink" href="#introduction" title="Link to this heading">¶</a></h4>
<p>The Newick format can be used for index construction
in combination with the <code class="docutils literal notranslate"><span class="pre">-A</span></code> parameter.
Names of files with sequences will be inferred from the names of leaves
as <code class="docutils literal notranslate"><span class="pre">[node_name].fa</span></code>.
If names of internal nodes are not specified in the original tree, they will be assigned automatically
as the lexigraphically minimal name of children’s names with incremented ID.
Branch lenghts are ignored.</p>
</section>
<section id="specification">
<h4>Specification<a class="headerlink" href="#specification" title="Link to this heading">¶</a></h4>
<p>See specifications of Newick on the
<a class="reference external" href="http://evolution.genetics.washington.edu/phylip/newicktree.html">Phylip website</a>
or on
<a class="reference external" href="https://en.wikipedia.org/wiki/Newick_format">Wikipedia</a>.</p>
</section>
<section id="examples">
<h4>Examples<a class="headerlink" href="#examples" title="Link to this heading">¶</a></h4>
<p>A Newick tree with named leaves:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">((</span><span class="n">n1</span><span class="p">,</span><span class="n">n2</span><span class="p">,</span><span class="n">n3</span><span class="p">),(</span><span class="n">n5</span><span class="p">,</span><span class="n">n6</span><span class="p">));</span>
</pre></div>
</div>
<p>A Newick tree with named nodes:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">((</span><span class="n">n1</span><span class="p">,</span><span class="n">n2</span><span class="p">)</span><span class="n">o1</span><span class="p">,(</span><span class="n">n3</span><span class="p">,</span><span class="n">n4</span><span class="p">,</span><span class="n">n5</span><span class="p">)</span><span class="n">o2</span><span class="p">)</span><span class="n">p1</span><span class="p">;</span>
</pre></div>
</div>
<p>A Newick tree with automatically assigned names of internal node names:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">((</span><span class="n">n1</span><span class="p">,</span><span class="n">n2</span><span class="p">,</span><span class="n">n3</span><span class="p">)</span><span class="n">n1</span><span class="o">-</span><span class="n">up1</span><span class="p">,(</span><span class="n">n4</span><span class="p">,</span><span class="n">n5</span><span class="p">)</span><span class="n">n4</span><span class="o">-</span><span class="n">up1</span><span class="p">)</span><span class="n">n1</span><span class="o">-</span><span class="n">up2</span><span class="p">;</span>
</pre></div>
</div>
</section>
</section>
<section id="nhx-trees">
<span id="index-1"></span><h3>NHX trees<a class="headerlink" href="#nhx-trees" title="Link to this heading">¶</a></h3>
<section id="id1">
<h4>Introduction<a class="headerlink" href="#id1" title="Link to this heading">¶</a></h4>
<p><a class="reference external" href="https://sites.google.com/site/cmzmasek/home/software/forester/nhx">New Hampshire X Format</a>
is parsed using the <a class="reference external" href="http://etetoolkit.org/">ETE3 library</a> (see specification of <a class="reference external" href="http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees">Format 1</a>).</p>
</section>
<section id="id2">
<h4>Specification<a class="headerlink" href="#id2" title="Link to this heading">¶</a></h4>
<blockquote>
<div><table class="docutils align-default" id="id20">
<caption><span class="caption-text">NHX attributes</span><a class="headerlink" href="#id20" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 20.6%" />
<col style="width: 20.6%" />
<col style="width: 58.8%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Attribute</p></th>
<th class="head"><p>Type</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>(name)</p></td>
<td><p>string</p></td>
<td><p>Node name (typically the TaxID of the node). The names should be unique and must not contain <code class="docutils literal notranslate"><span class="pre">@</span></code>.</p></td>
</tr>
<tr class="row-odd"><td><p>path</p></td>
<td><p>string</p></td>
<td><p>Files with genomic sequences, separated by <code class="docutils literal notranslate"><span class="pre">@</span></code> (relative paths from the directory of the tree). Only for leaves.</p></td>
</tr>
<tr class="row-even"><td><p>fastapath</p></td>
<td><p>string</p></td>
<td><p>Deprecated (use <cite>path</cite> instead).</p></td>
</tr>
<tr class="row-odd"><td><p>rank</p></td>
<td><p>string/int</p></td>
<td><p>Taxonomic rank.</p></td>
</tr>
<tr class="row-even"><td><p>dist</p></td>
<td><p>float</p></td>
<td><p>To be ignored (an internal parameter of ETE3).</p></td>
</tr>
<tr class="row-odd"><td><p>support</p></td>
<td><p>float</p></td>
<td><p>To be ignored (an internal parameter of ETE3).</p></td>
</tr>
<tr class="row-even"><td><p>kmers_full</p></td>
<td><p>integer</p></td>
<td><p>Number of k-mers associated with this node. Added automatically during index construction.</p></td>
</tr>
<tr class="row-odd"><td><p>kmers_reduced</p></td>
<td><p>integer</p></td>
<td><p>Number of k-mers represented by this node. Added automatically during index construction.</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
<section id="example">
<h4>Example<a class="headerlink" href="#example" title="Link to this heading">¶</a></h4>
<p>Previous tree after autocompleting to NHX:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">(((</span><span class="n">n1</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">path</span><span class="o">=</span><span class="n">n1</span><span class="o">.</span><span class="n">fa</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">],</span><span class="n">n2</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">path</span><span class="o">=</span><span class="n">n2</span><span class="o">.</span><span class="n">fa</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">])</span><span class="n">o1</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">],(</span><span class="n">n3</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">path</span><span class="o">=</span><span class="n">n3</span><span class="o">.</span><span class="n">fa</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">],</span><span class="n">n4</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">path</span><span class="o">=</span><span class="n">n4</span><span class="o">.</span><span class="n">fa</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">],</span><span class="n">n5</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">path</span><span class="o">=</span><span class="n">n5</span><span class="o">.</span><span class="n">fa</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">])</span><span class="n">o2</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">])</span><span class="n">p1</span><span class="p">:</span><span class="mi">0</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">0.0</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">])</span><span class="n">merge_root</span><span class="p">:</span><span class="mi">1</span><span class="p">[</span><span class="o">&&</span><span class="n">NHX</span><span class="p">:</span><span class="n">dist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">:</span><span class="n">support</span><span class="o">=</span><span class="mf">1.0</span><span class="p">];</span>
</pre></div>
</div>
</section>
</section>
<section id="sequences">
<h3>Sequences<a class="headerlink" href="#sequences" title="Link to this heading">¶</a></h3>
<p>Input sequences can be provided in the FASTA or FASTQ formats. Any non-<code class="docutils literal notranslate"><span class="pre">ACGT</span></code> characters are treated as
unknown nucleotides and k-mers containing them thus discarded.
Sequence names are ignored.</p>
</section>
</section>
<section id="assignments">
<h2><span class="section-number">8.2. </span>Assignments<a class="headerlink" href="#assignments" title="Link to this heading">¶</a></h2>
<section id="read-assignments-in-sam-bam">
<span id="index-2"></span><h3>Read assignments in SAM/BAM<a class="headerlink" href="#read-assignments-in-sam-bam" title="Link to this heading">¶</a></h3>
<section id="id3">
<h4>Introduction<a class="headerlink" href="#id3" title="Link to this heading">¶</a></h4>
<p>ProPhyle uses <a class="reference external" href="http://samtools.github.io/hts-specs/">SAM/BAM</a> as
the main format for reporting the final assignments, i.e.,
the output of classification.</p>
</section>
<section id="id4">
<h4>Specification<a class="headerlink" href="#id4" title="Link to this heading">¶</a></h4>
<blockquote>
<div><table class="docutils align-default" id="id21">
<caption><span class="caption-text">ProPhyle SAM headers</span><a class="headerlink" href="#id21" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 25.0%" />
<col style="width: 75.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Tag</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>HD</p></td>
<td><p>Version of SAM.</p></td>
</tr>
<tr class="row-odd"><td><p>PG</p></td>
<td><p>Version of ProPhyle.</p></td>
</tr>
<tr class="row-even"><td><p>SQ</p></td>
<td><p>Description of a leaf. <em>SN:</em> Name of the node. <em>LN:</em> a fake length. <em>UR:</em> Name of the original FASTA file. <em>SP:</em> Name of the species (if present in the tree).</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
<div class="line-block">
<div class="line"><br /></div>
</div>
<blockquote>
<div><table class="docutils align-default" id="id22">
<caption><span class="caption-text">ProPhyle SAM fields</span><a class="headerlink" href="#id22" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 11.5%" />
<col style="width: 11.5%" />
<col style="width: 76.9%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Column</p></th>
<th class="head"><p>Name</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>QNAME</p></td>
<td><p>Query name.</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>FLAG</p></td>
<td><p><code class="docutils literal notranslate"><span class="pre">0</span></code> if assigned, <code class="docutils literal notranslate"><span class="pre">4</span></code> otherwise.</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>RNAME</p></td>
<td><p>Node name.</p></td>
</tr>
<tr class="row-odd"><td><p>4</p></td>
<td><p>POS</p></td>
<td><p><code class="docutils literal notranslate"><span class="pre">1</span></code> if assigned, unused (<code class="docutils literal notranslate"><span class="pre">0</span></code>) otherwise.</p></td>
</tr>
<tr class="row-even"><td><p>5</p></td>
<td><p>MAPQ</p></td>
<td><p><code class="docutils literal notranslate"><span class="pre">60</span></code> if assigned, unused (<code class="docutils literal notranslate"><span class="pre">0</span></code>) otherwise.</p></td>
</tr>
<tr class="row-odd"><td><p>6</p></td>
<td><p>CIGAR</p></td>
<td><p>Coverage bit-mask encoded as a CIGAR string if assigned, unused (<code class="docutils literal notranslate"><span class="pre">*</span></code>) otherwise. For instance, <cite>7=3X3=</cite> means <cite>1111111000111</cite>.</p></td>
</tr>
<tr class="row-even"><td><p>7</p></td>
<td><p>RNEXT</p></td>
<td><p>Unused (<code class="docutils literal notranslate"><span class="pre">*</span></code>).</p></td>
</tr>
<tr class="row-odd"><td><p>8</p></td>
<td><p>PNEXT</p></td>
<td><p>Unused (<code class="docutils literal notranslate"><span class="pre">0</span></code>).</p></td>
</tr>
<tr class="row-even"><td><p>9</p></td>
<td><p>TLEN</p></td>
<td><p>Unused (<code class="docutils literal notranslate"><span class="pre">0</span></code>).</p></td>
</tr>
<tr class="row-odd"><td><p>10</p></td>
<td><p>SEQ</p></td>
<td><p>Sequence of bases if <code class="docutils literal notranslate"><span class="pre">-P</span></code>, unused (<code class="docutils literal notranslate"><span class="pre">*</span></code>) otherwise.</p></td>
</tr>
<tr class="row-even"><td><p>11</p></td>
<td><p>QUAL</p></td>
<td><p>Base qualities if <code class="docutils literal notranslate"><span class="pre">-P</span></code>, unused (<code class="docutils literal notranslate"><span class="pre">*</span></code>) otherwise.</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
<div class="line-block">
<div class="line"><br /></div>
</div>
<blockquote>
<div><table class="docutils align-default" id="id23">
<caption><span class="caption-text">ProPhyle SAM tags</span><a class="headerlink" href="#id23" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 10.7%" />
<col style="width: 10.7%" />
<col style="width: 53.6%" />
<col style="width: 25.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Tag</p></th>
<th class="head"><p>Type</p></th>
<th class="head"><p>Description</p></th>
<th class="head"><p>Range</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>ln</p></td>
<td><p>integer</p></td>
<td><p>Read length.</p></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>h1</p></td>
<td><p>integer</p></td>
<td><p>Number of shared k-mers.</p></td>
<td><p><span class="math">\{1, \ldots, |query|-k+1\}</span></p></td>
</tr>
<tr class="row-even"><td><p>h2</p></td>
<td><p>float</p></td>
<td><p>Proportion of hits in the reference.</p></td>
<td><p><span class="math">(0,1]</span></p></td>
</tr>
<tr class="row-odd"><td><p>hf</p></td>
<td><p>float</p></td>
<td><p>Proportion of hits in the query.</p></td>
<td><p><span class="math">(0,1]</span></p></td>
</tr>
<tr class="row-even"><td><p>c1</p></td>
<td><p>integer</p></td>
<td><p>Number of covered positions in the query.</p></td>
<td><p><span class="math">\{k, \ldots, |query|\}</span></p></td>
</tr>
<tr class="row-odd"><td><p>c2</p></td>
<td><p>float</p></td>
<td><p>Normalized number of covered positions in the query.</p></td>
<td><p><span class="math">(0,1]</span></p></td>
</tr>
<tr class="row-even"><td><p>cf</p></td>
<td><p>float</p></td>
<td><p>Proportion of covered positions in the query.</p></td>
<td><p><span class="math">(0,1]</span></p></td>
</tr>
<tr class="row-odd"><td><p>is</p></td>
<td><p>int</p></td>
<td><p>Number of reported assignments (nodes) for the query.</p></td>
<td><p><span class="math">\{1, \ldots, |leaves|\}</span></p></td>
</tr>
<tr class="row-even"><td><p>ii</p></td>
<td><p>int</p></td>
<td><p>ID of the curent assignment.</p></td>
<td><p><span class="math">\{1, \ldots, is\}</span></p></td>
</tr>
<tr class="row-odd"><td><p>hc</p></td>
<td><p>string</p></td>
<td><p>Hit bit-mask encoded as a CIGAR string. For instance, <cite>7=1X3=</cite> means <cite>11111110111</cite>.</p></td>
<td></td>
</tr>
</tbody>
</table>
</div></blockquote>
<div class="line-block">
<div class="line"><br /></div>
</div>
</section>
</section>
<section id="read-assignments-in-a-kraken-like-format">
<h3>Read assignments in a Kraken-like format<a class="headerlink" href="#read-assignments-in-a-kraken-like-format" title="Link to this heading">¶</a></h3>
<section id="id5">
<h4>Introduction<a class="headerlink" href="#id5" title="Link to this heading">¶</a></h4>
<p>ProPhyle uses a format similar to the <a class="reference external" href="https://ccb.jhu.edu/software/kraken/MANUAL.html#output-format">Kraken output</a> for reporting k-mer matches by <a class="reference external" href="https://github.com/prophyle/prophyle_index">ProPhyle Index</a>. It can also use this format
for reporting the final assignments.</p>
</section>
<section id="id6">
<h4>Specification<a class="headerlink" href="#id6" title="Link to this heading">¶</a></h4>
<blockquote>
<div><table class="docutils align-default" id="id24">
<caption><span class="caption-text">Kraken-like format</span><a class="headerlink" href="#id24" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 10.7%" />
<col style="width: 89.3%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Column</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>C / U (classified / unclassified)</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>Query name</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>Final assignments – a comma separated list of node names</p></td>
</tr>
<tr class="row-odd"><td><p>4</p></td>
<td><p>Query length</p></td>
</tr>
<tr class="row-even"><td><p>5</p></td>
<td><p>K-mer mappings: a space-delimited lists of mappings. A single mapping is of the form <code class="docutils literal notranslate"><span class="pre">comma_delimited_list_of_nodes:length</span></code>. Pseudo-nodes <code class="docutils literal notranslate"><span class="pre">A</span></code> and <code class="docutils literal notranslate"><span class="pre">0</span></code> are used for k-mers with a non-<code class="docutils literal notranslate"><span class="pre">ACGT</span></code> nucleotide and without any mapping, respectively.</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
<section id="id7">
<h4>Examples<a class="headerlink" href="#id7" title="Link to this heading">¶</a></h4>
<p>Assigned k-mers, no sequences:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">U</span> <span class="n">read3</span> <span class="mi">0</span> <span class="mi">8</span> <span class="n">left</span><span class="p">,</span><span class="n">right</span><span class="p">:</span><span class="mi">1</span> <span class="n">A</span><span class="p">:</span><span class="mi">3</span> <span class="mi">0</span><span class="p">:</span><span class="mi">1</span> <span class="n">right</span><span class="p">:</span><span class="mi">1</span>
</pre></div>
</div>
<p>Assigned k-mers, version with sequences and base qualities:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">U</span> <span class="n">read3</span> <span class="mi">0</span> <span class="mi">8</span> <span class="n">left</span><span class="p">,</span><span class="n">right</span><span class="p">:</span><span class="mi">1</span> <span class="n">A</span><span class="p">:</span><span class="mi">3</span> <span class="mi">0</span><span class="p">:</span><span class="mi">1</span> <span class="n">right</span><span class="p">:</span><span class="mi">1</span> <span class="n">CTTNGTTT</span> <span class="n">IGIIIIHI</span>
</pre></div>
</div>
</section>
</section>
</section>
<section id="abundances-estimates-experimental">
<h2><span class="section-number">8.3. </span>Abundances estimates (experimental)<a class="headerlink" href="#abundances-estimates-experimental" title="Link to this heading">¶</a></h2>
<section id="abundances-in-the-kraken-report-format">
<span id="index-3"></span><h3>Abundances in the Kraken report format<a class="headerlink" href="#abundances-in-the-kraken-report-format" title="Link to this heading">¶</a></h3>
<section id="id8">
<h4>Introduction<a class="headerlink" href="#id8" title="Link to this heading">¶</a></h4>
</section>
<section id="id9">
<h4>Specification<a class="headerlink" href="#id9" title="Link to this heading">¶</a></h4>
<p><a class="reference external" href="https://ccb.jhu.edu/software/kraken/MANUAL.html#sample-reports">kraken-report</a> format:</p>
<blockquote>
<div><table class="docutils align-default" id="id25">
<caption><span class="caption-text">Kraken report format</span><a class="headerlink" href="#id25" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 20.0%" />
<col style="width: 80.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Column</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>Percentage of reads covered by the clade rooted at this taxon</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>Number of reads covered by the clade rooted at this taxon</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>Number of reads assigned directly to this taxon</p></td>
</tr>
<tr class="row-odd"><td><p>4</p></td>
<td><p>A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply ‘-‘.</p></td>
</tr>
<tr class="row-even"><td><p>5</p></td>
<td><p>NCBI taxonomy ID</p></td>
</tr>
<tr class="row-odd"><td><p>6</p></td>
<td><p>Indented scientific name</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
</section>
<section id="abundances-in-the-metaphlan2-report-format">
<span id="index-4"></span><h3>Abundances in the MetaPhlAn2 report format<a class="headerlink" href="#abundances-in-the-metaphlan2-report-format" title="Link to this heading">¶</a></h3>
<section id="id10">
<h4>Introduction<a class="headerlink" href="#id10" title="Link to this heading">¶</a></h4>
<p><a class="reference external" href="http://huttenhower.sph.harvard.edu/metaphlan2">MetaPhlAn2</a> is a computational tool for profiling the composition of microbial communities from metagenomic sequencing data.</p>
</section>
<section id="id11">
<h4>Specification<a class="headerlink" href="#id11" title="Link to this heading">¶</a></h4>
<p><a class="reference external" href="https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2#rst-header-output-files">MetaPhlAn2 report format</a></p>
<blockquote>
<div><table class="docutils align-default" id="id26">
<caption><span class="caption-text">Metaphlan 2 report format</span><a class="headerlink" href="#id26" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 20.0%" />
<col style="width: 80.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Column</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>Clades, ranging from taxonomic kingdoms (Bacteria, Archaea, etc.) through species</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>The taxonomic level of each clade is prefixed to indicate its level: Kingdom: <code class="docutils literal notranslate"><span class="pre">k__</span></code>, Phylum: <code class="docutils literal notranslate"><span class="pre">p__</span></code>, Class: <code class="docutils literal notranslate"><span class="pre">c__</span></code>, Order: <code class="docutils literal notranslate"><span class="pre">o__</span></code>, Family: <code class="docutils literal notranslate"><span class="pre">f__</span></code>, Genus: <code class="docutils literal notranslate"><span class="pre">g__</span></code>, Species: <code class="docutils literal notranslate"><span class="pre">s__</span></code></p></td>
</tr>
</tbody>
</table>
</div></blockquote>
<p>Since sequence-based profiling is relative and does not provide absolute cellular abundance measures, clades are hierarchically summed. Each level will sum to 100%; that is, the sum of all kindom-level clades is 100%, the sum of all genus-level clades (including unclassified) is also 100%, and so forth. OTU equivalents can be extracted by using only the species-level <code class="docutils literal notranslate"><span class="pre">s__</span></code> clades from this file (again, making sure to include clades unclassified at this level).</p>
</section>
</section>
<section id="abundances-in-the-centrifuge-report-format">
<span id="index-5"></span><h3>Abundances in the Centrifuge report format<a class="headerlink" href="#abundances-in-the-centrifuge-report-format" title="Link to this heading">¶</a></h3>
<section id="id12">
<h4>Introduction<a class="headerlink" href="#id12" title="Link to this heading">¶</a></h4>
<p><a class="reference external" href="https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-summary-output-the-default-filename-is-centrifuge_report.tsv">Centrifuge</a> format.</p>
</section>
<section id="id13">
<h4>Specification<a class="headerlink" href="#id13" title="Link to this heading">¶</a></h4>
<blockquote>
<div><table class="docutils align-default" id="id27">
<caption><span class="caption-text">Centrifuge format</span><a class="headerlink" href="#id27" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 20.0%" />
<col style="width: 80.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Column</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>name of a genome, or the name corresponding to a taxonomic ID (the second column) at a rank higher than the strain (e.g., Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis).</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>taxonomic ID (e.g., 36870).</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>taxonomic rank (e.g., leaf).</p></td>
</tr>
<tr class="row-odd"><td><p>4</p></td>
<td><p>number of k-mers propagated up to the node (e.g., 703004).</p></td>
</tr>
<tr class="row-even"><td><p>5</p></td>
<td><p>number of reads classified to this node including multi-classified reads (divided by the number of assignments, e.g., 5981.37)</p></td>
</tr>
<tr class="row-odd"><td><p>6</p></td>
<td><p>number of reads uniquely classified to this genomic sequence (e.g., 5964)</p></td>
</tr>
<tr class="row-even"><td><p>7</p></td>
<td><p>unused</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
<section id="id14">
<h4>Example<a class="headerlink" href="#id14" title="Link to this heading">¶</a></h4>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#name taxID taxRank kmerCount numReads numUniqueReads abundance</span>
<span class="n">Wigglesworthia</span> <span class="n">glossinidia</span> <span class="n">endosymbiont</span> <span class="n">of</span> <span class="n">Glossina</span> <span class="n">brevipalpis</span> <span class="mi">36870</span> <span class="n">leaf</span> <span class="mi">703004</span> <span class="mf">5981.37</span> <span class="mi">5964</span> <span class="mi">0</span>
</pre></div>
</div>
</section>
</section>
</section>
<section id="internal-prophyle-formats">
<h2><span class="section-number">8.4. </span>Internal ProPhyle formats<a class="headerlink" href="#internal-prophyle-formats" title="Link to this heading">¶</a></h2>
<section id="index-6">
<span id="id15"></span><h3>ProPhyle Index<a class="headerlink" href="#index-6" title="Link to this heading">¶</a></h3>
<section id="id16">
<h4>Introduction<a class="headerlink" href="#id16" title="Link to this heading">¶</a></h4>
<p>ProPhyle index directory contains a BWA index,
a k-LCP array and several auxiliary files.</p>
</section>
<section id="id17">
<h4>Specification<a class="headerlink" href="#id17" title="Link to this heading">¶</a></h4>
<blockquote>
<div><table class="docutils align-default" id="id28">
<caption><span class="caption-text">ProPhyle index</span><a class="headerlink" href="#id28" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 20.0%" />
<col style="width: 80.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>File name</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa</span></code></p></td>
<td><p>Assembled contigs, name of sequences are of the following format: <code class="docutils literal notranslate"><span class="pre">[node_name]@c[contig_id]</span></code></p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.amb</span></code></p></td>
<td><p>List of ambiguous nucleotides, no values</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.ann</span></code></p></td>
<td><p>List of contigs and their starting positions in the master string</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.[k].klcp</span></code></p></td>
<td><p>k-LCP array</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.bwt</span></code></p></td>
<td><p>Burrows-Wheeler Transform of the master string (merged sequences + reverse completement) + OCC table (BWA format)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.kmers.tsv</span></code></p></td>
<td><p>k-mer statistics, format: <code class="docutils literal notranslate"><span class="pre">[node_name].[full|reduced].fa</span>        <span class="pre">[#kmers]</span></code>, where <code class="docutils literal notranslate"><span class="pre">full</span></code> refers to all associated k-mers and <code class="docutils literal notranslate"><span class="pre">reduced</span></code> to represented k-mers</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.pac</span></code></p></td>
<td><p>Packed sequences (BWA format)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.sa</span></code></p></td>
<td><p>Sampled suffix array (BWA format)</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.json</span></code></p></td>
<td><p>Index parameters: k-mer size (<code class="docutils literal notranslate"><span class="pre">k</span></code>), ProPhyle version (<code class="docutils literal notranslate"><span class="pre">prophyle-version</span></code>, <code class="docutils literal notranslate"><span class="pre">prophyle-revision</span></code>, <code class="docutils literal notranslate"><span class="pre">prophyle-commit</span></code>)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">log.txt</span></code></p></td>
<td><p>Log</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">tree.nw</span></code></p></td>
<td><p>Phylogenetic tree adjusted for classification</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">tree.preliminary.nw</span></code></p></td>
<td><p>Phylogenetic tree before adjusting</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
</section>
<section id="compressed-prophyle-index-for-transmission">
<span id="index-7"></span><h3>Compressed ProPhyle index for transmission<a class="headerlink" href="#compressed-prophyle-index-for-transmission" title="Link to this heading">¶</a></h3>
<section id="id18">
<h4>Introduction<a class="headerlink" href="#id18" title="Link to this heading">¶</a></h4>
<p>ProPhyle can create a <code class="docutils literal notranslate"><span class="pre">.tar.gz</span></code> archive with the a subset of the index files so
that the original index can be derived.</p>
</section>
<section id="id19">
<h4>Specification<a class="headerlink" href="#id19" title="Link to this heading">¶</a></h4>
<p>The archive contains the following subset of the original index files:</p>
<blockquote>
<div><table class="docutils align-default" id="id29">
<caption><span class="caption-text">Compressed ProPhyle index</span><a class="headerlink" href="#id29" title="Link to this table">¶</a></caption>
<colgroup>
<col style="width: 20.0%" />
<col style="width: 80.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>File name</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.amb</span></code></p></td>
<td><p>Identical</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.ann</span></code></p></td>
<td><p>Identical</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.bwt</span></code></p></td>
<td><p>Burrows-Wheeler Transform <em>without</em> the OCC table (BWA format, before <code class="docutils literal notranslate"><span class="pre">bwa</span> <span class="pre">bwtupdate</span></code>)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">index.fa.kmers.tsv</span></code></p></td>
<td><p>Identical</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">index.json</span></code></p></td>
<td><p>Identical</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">tree.nw</span></code></p></td>
<td><p>Identical</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">tree.preliminary.nw</span></code></p></td>
<td><p>Identical</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
</section>
</section>
</section>
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