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<div class="section" id="tutorials">
<h1>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this headline">¶</a></h1>
<div class="section" id="simple-distance-estimation">
<h2>Simple distance estimation<a class="headerlink" href="#simple-distance-estimation" title="Permalink to this headline">¶</a></h2>
<p>Download example <em>E. coli</em> genomes:</p>
<div class="line-block">
<div class="line"><a class="reference external" href="https://gembox.cbcb.umd.edu/mash/genome1.fna">genome1.fna</a></div>
<div class="line"><a class="reference external" href="https://gembox.cbcb.umd.edu/mash/genome2.fna">genome2.fna</a></div>
</div>
<p>Run:</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">mash</span> <span class="n">dist</span> <span class="n">genome1</span><span class="o">.</span><span class="n">fna</span> <span class="n">genome2</span><span class="o">.</span><span class="n">fna</span>
</pre></div>
</div>
<p>The results are tab delimited lists of Reference-ID, Query-ID, Mash-distance,
P-value, and Matching-hashes:</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">genome1</span><span class="o">.</span><span class="n">fna</span> <span class="n">genome2</span><span class="o">.</span><span class="n">fna</span> <span class="mf">0.0222766</span> <span class="mi">0</span> <span class="mi">456</span><span class="o">/</span><span class="mi">1000</span>
</pre></div>
</div>
</div>
<div class="section" id="saving-time-by-sketching-first">
<h2>Saving time by sketching first<a class="headerlink" href="#saving-time-by-sketching-first" title="Permalink to this headline">¶</a></h2>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">mash</span> <span class="n">sketch</span> <span class="n">genome1</span><span class="o">.</span><span class="n">fna</span>
<span class="n">mash</span> <span class="n">sketch</span> <span class="n">genome2</span><span class="o">.</span><span class="n">fna</span>
<span class="n">mash</span> <span class="n">dist</span> <span class="n">genome1</span><span class="o">.</span><span class="n">fna</span><span class="o">.</span><span class="n">msh</span> <span class="n">genome2</span><span class="o">.</span><span class="n">fna</span><span class="o">.</span><span class="n">msh</span>
</pre></div>
</div>
</div>
<div class="section" id="pairwise-comparisons-with-compound-sketch-files">
<h2>Pairwise comparisons with compound sketch files<a class="headerlink" href="#pairwise-comparisons-with-compound-sketch-files" title="Permalink to this headline">¶</a></h2>
<p>Download additional example <em>E. coli</em> genome:</p>
<div class="line-block">
<div class="line"><a class="reference external" href="https://gembox.cbcb.umd.edu/mash/genome3.fna">genome3.fna</a></div>
</div>
<p>Sketch the first two genomes to create a combined archive, use <code class="code docutils literal"><span class="pre">mash</span> <span class="pre">info</span></code>
to verify its contents, and estimate pairwise distances:</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">mash</span> <span class="n">sketch</span> <span class="o">-</span><span class="n">o</span> <span class="n">reference</span> <span class="n">genome1</span><span class="o">.</span><span class="n">fna</span> <span class="n">genome2</span><span class="o">.</span><span class="n">fna</span>
<span class="n">mash</span> <span class="n">info</span> <span class="n">reference</span><span class="o">.</span><span class="n">msh</span>
<span class="n">mash</span> <span class="n">dist</span> <span class="n">reference</span><span class="o">.</span><span class="n">msh</span> <span class="n">genome3</span><span class="o">.</span><span class="n">fna</span>
</pre></div>
</div>
<p>This will estimate the distance from each query (which there is one of) to each
reference (which there are two of in the sketch file):</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">genome1</span><span class="o">.</span><span class="n">fna</span> <span class="n">genome3</span><span class="o">.</span><span class="n">fna</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1000</span><span class="o">/</span><span class="mi">1000</span>
<span class="n">genome2</span><span class="o">.</span><span class="n">fna</span> <span class="n">genome3</span><span class="o">.</span><span class="n">fna</span> <span class="mf">0.0222766</span> <span class="mi">0</span> <span class="mi">456</span><span class="o">/</span><span class="mi">1000</span>
</pre></div>
</div>
</div>
<div class="section" id="querying-read-sets-against-an-existing-refseq-sketch">
<h2>Querying read sets against an existing RefSeq sketch<a class="headerlink" href="#querying-read-sets-against-an-existing-refseq-sketch" title="Permalink to this headline">¶</a></h2>
<p>Download and gunzip the pre-sketched RefSeq archive (reads not provided here;
10x-100x coverage of a single genome with any sequencing technology should
work):</p>
<p><a class="reference external" href="http://gembox.cbcb.umd.edu/mash/RefSeqSketches.msh.gz">RefSeqSketches.msh.gz</a></p>
<p>Concatenate paired ends (this could also be piped to <code class="code docutils literal"><span class="pre">mash</span></code> to save space by
specifying <code class="code docutils literal"><span class="pre">-</span></code> for standard input, zipped or unzipped):</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="n">reads_1</span><span class="o">.</span><span class="n">fastq</span> <span class="n">read_2</span><span class="o">.</span><span class="n">fastq</span> <span class="o">></span> <span class="n">reads</span><span class="o">.</span><span class="n">fastq</span>
</pre></div>
</div>
<p>Sketch the reads, using <code class="code docutils literal"><span class="pre">-m</span> <span class="pre">2</span></code> to improve results
by ignoring single-copy k-mers, which are more likely to be erroneous:</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">mash</span> <span class="n">sketch</span> <span class="o">-</span><span class="n">m</span> <span class="mi">2</span> <span class="o">-</span><span class="n">k</span> <span class="mi">16</span> <span class="o">-</span><span class="n">s</span> <span class="mi">400</span> <span class="n">reads</span><span class="o">.</span><span class="n">fastq</span>
</pre></div>
</div>
<p>Run <code class="code docutils literal"><span class="pre">mash</span> <span class="pre">dist</span></code> with the RefSeq archive as the reference and the read
sketch as the query:</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">mash</span> <span class="n">dist</span> <span class="n">RefSeqSketches</span><span class="o">.</span><span class="n">msh</span> <span class="n">reads</span><span class="o">.</span><span class="n">fastq</span><span class="o">.</span><span class="n">msh</span> <span class="o">></span> <span class="n">distances</span><span class="o">.</span><span class="n">tab</span>
</pre></div>
</div>
<p>Sort the results to see the top hits and their p-values:</p>
<div class="code highlight-default"><div class="highlight"><pre><span></span><span class="n">sort</span> <span class="o">-</span><span class="n">gk3</span> <span class="n">distances</span><span class="o">.</span><span class="n">tab</span> <span class="o">|</span> <span class="n">head</span>
</pre></div>
</div>
</div>
<div class="section" id="building-a-custom-refseq-database">
<h2>Building a custom RefSeq database<a class="headerlink" href="#building-a-custom-refseq-database" title="Permalink to this headline">¶</a></h2>
<p>To create the RefSeq Mash database, genomes were downloaded from NCBI
(<code class="code docutils literal"><span class="pre">ftp.ncbi.nlm.nih.gov/refseq/release/complete</span></code>, fasta sequence and
GenBank annotations for <code class="code docutils literal"><span class="pre">genomic</span></code>), and the
<a class="reference external" href="https://github.com/ondovb/refseqCollate/releases">refseqCollate</a> utility was
used to collate contigs/chromosomes into individual fasta files per genome.
Groups of these files were sketched in parallel and then pasted together with
<code class="code docutils literal"><span class="pre">mash</span> <span class="pre">paste</span></code>. This process could be repeated for more current or custom
databases.</p>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Tutorials</a><ul>
<li><a class="reference internal" href="#simple-distance-estimation">Simple distance estimation</a></li>
<li><a class="reference internal" href="#saving-time-by-sketching-first">Saving time by sketching first</a></li>
<li><a class="reference internal" href="#pairwise-comparisons-with-compound-sketch-files">Pairwise comparisons with compound sketch files</a></li>
<li><a class="reference internal" href="#querying-read-sets-against-an-existing-refseq-sketch">Querying read sets against an existing RefSeq sketch</a></li>
<li><a class="reference internal" href="#building-a-custom-refseq-database">Building a custom RefSeq database</a></li>
</ul>
</li>
</ul>
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