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<section id="finaletoolkit">
<h1>FinaleToolkit<a class="headerlink" href="#finaletoolkit" title="Link to this heading">#</a></h1>
<section id="about">
<h2>About<a class="headerlink" href="#about" title="Link to this heading">#</a></h2>
<p>FinaleToolkit (FragmentatIoN AnaLysis of cEll-free DNA Toolkit) is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.</p>
<ul class="simple">
<li><p><strong>Website:</strong> <a class="reference external" href="https://epifluidlab.github.io/finaletoolkit-docs/">https://epifluidlab.github.io/finaletoolkit-docs/</a></p></li>
<li><p><strong>PyPI:</strong> <a class="reference external" href="https://pypi.org/project/finaletoolkit/">https://pypi.org/project/finaletoolkit/</a></p></li>
<li><p><strong>Documentation:</strong> <a class="reference external" href="https://epifluidlab.github.io/finaletoolkit-docs/documentation">https://epifluidlab.github.io/finaletoolkit-docs/documentation</a></p></li>
<li><p><strong>Source code:</strong> <a class="github reference external" href="https://github.com/epifluidlab/finaletoolkit">epifluidlab/finaletoolkit</a></p></li>
<li><p><strong>Changelog:</strong> <a class="github reference external" href="https://github.com/epifluidlab/FinaleToolkit/blob/main/CHANGELOG.md">epifluidlab/FinaleToolkit</a></p></li>
<li><p><strong>Bug reports:</strong> <a class="github reference external" href="https://github.com/epifluidlab/finaletoolkit/issues">epifluidlab/finaletoolkit#issues</a></p></li>
</ul>
</section>
<section id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Link to this heading">#</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="documentation/index.html">FinaleToolkit Documentation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/index.html">User Guide</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/cli_reference/index.html">CLI</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/index.html">API</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="documentation/user_guide/index.html">User Guide</a><ul>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/what.html">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/inputdata.html">Input Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/features.html">Features</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/installation.html">Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/structure.html">Structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/intersectpolicy.html">Intersect Policy</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/quickstart.html">Quickstart</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/user_guide/help.html">Help</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="documentation/cli_reference/index.html">CLI</a><ul>
<li class="toctree-l2"><a class="reference internal" href="documentation/cli_reference/index.html#named-arguments">Named Arguments</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/cli_reference/index.html#Sub-commands">Sub-commands</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="documentation/api_reference/index.html">API</a><ul>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/basicfeatures.html">Basic Features</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/wps.html">Window Protection Score (WPS)</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/delfi.html">DELFI</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/endmotifs.html">End-Motifs</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/cleavageprofile.html">Cleavage Profile</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/fragfile.html">Frag File Utilities</a></li>
<li class="toctree-l2"><a class="reference internal" href="documentation/api_reference/genomeutils.html">Genome Utilities</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="citations">
<h2>Citations<a class="headerlink" href="#citations" title="Link to this heading">#</a></h2>
<p>If FinaleToolkit is integral to a scientific publication, please cite it. A paper describing FinaleToolkit has been written. Here is a ready-made BibTeX entry:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@article</span> <span class="p">{</span><span class="n">Li2024</span><span class="mf">.05.29.596414</span><span class="p">,</span>
<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">Li</span><span class="p">,</span> <span class="n">James</span> <span class="n">W</span><span class="o">.</span> <span class="ow">and</span> <span class="n">Bandaru</span><span class="p">,</span> <span class="n">Ravi</span> <span class="ow">and</span> <span class="n">Liu</span><span class="p">,</span> <span class="n">Yaping</span><span class="p">},</span>
<span class="n">title</span> <span class="o">=</span> <span class="p">{</span><span class="n">FinaleToolkit</span><span class="p">:</span> <span class="n">Accelerating</span> <span class="n">Cell</span><span class="o">-</span><span class="n">Free</span> <span class="n">DNA</span> <span class="n">Fragmentation</span> <span class="n">Analysis</span> <span class="k">with</span> <span class="n">a</span> <span class="n">High</span><span class="o">-</span><span class="n">Speed</span> <span class="n">Computational</span> <span class="n">Toolkit</span><span class="p">},</span>
<span class="n">elocation</span><span class="o">-</span><span class="nb">id</span> <span class="o">=</span> <span class="p">{</span><span class="mf">2024.05.29.596414</span><span class="p">},</span>
<span class="n">year</span> <span class="o">=</span> <span class="p">{</span><span class="mi">2024</span><span class="p">},</span>
<span class="n">doi</span> <span class="o">=</span> <span class="p">{</span><span class="mf">10.1101</span><span class="o">/</span><span class="mf">2024.05.29.596414</span><span class="p">},</span>
<span class="n">publisher</span> <span class="o">=</span> <span class="p">{</span><span class="n">Cold</span> <span class="n">Spring</span> <span class="n">Harbor</span> <span class="n">Laboratory</span><span class="p">},</span>
<span class="n">abstract</span> <span class="o">=</span> <span class="p">{</span><span class="n">Cell</span><span class="o">-</span><span class="n">free</span> <span class="n">DNA</span> <span class="p">(</span><span class="n">cfDNA</span><span class="p">)</span> <span class="n">fragmentation</span> <span class="n">pattern</span> <span class="n">represents</span> <span class="n">a</span> <span class="n">promising</span> <span class="n">non</span><span class="o">-</span><span class="n">invasive</span> <span class="n">biomarker</span> <span class="k">for</span> <span class="n">disease</span> <span class="n">diagnosis</span> <span class="ow">and</span> <span class="n">prognosis</span><span class="o">.</span> <span class="n">Numerous</span> <span class="n">fragmentation</span> <span class="n">features</span><span class="p">,</span> <span class="n">such</span> <span class="k">as</span> <span class="n">end</span> <span class="n">motif</span> <span class="ow">and</span> <span class="n">window</span> <span class="n">protection</span> <span class="n">score</span> <span class="p">(</span><span class="n">WPS</span><span class="p">),</span> <span class="n">have</span> <span class="n">been</span> <span class="n">characterized</span> <span class="ow">in</span> <span class="n">cfDNA</span> <span class="n">genomic</span> <span class="n">sequencing</span><span class="o">.</span> <span class="n">However</span><span class="p">,</span> <span class="n">the</span> <span class="n">analytical</span> <span class="n">tools</span> <span class="n">developed</span> <span class="ow">in</span> <span class="n">these</span> <span class="n">studies</span> <span class="n">are</span> <span class="n">often</span> <span class="ow">not</span> <span class="n">released</span> <span class="n">to</span> <span class="n">the</span> <span class="n">liquid</span> <span class="n">biopsy</span> <span class="n">community</span> <span class="ow">or</span> <span class="n">are</span> <span class="n">inefficient</span> <span class="k">for</span> <span class="n">genome</span><span class="o">-</span><span class="n">wide</span> <span class="n">analysis</span> <span class="ow">in</span> <span class="n">large</span> <span class="n">datasets</span><span class="o">.</span> <span class="n">To</span> <span class="n">address</span> <span class="n">this</span> <span class="n">gap</span><span class="p">,</span> <span class="n">we</span> <span class="n">have</span> <span class="n">developed</span> <span class="n">FinaleToolkit</span><span class="p">,</span> <span class="n">a</span> <span class="n">fast</span> <span class="ow">and</span> <span class="n">memory</span> <span class="n">efficient</span> <span class="n">Python</span> <span class="n">package</span> <span class="n">designed</span> <span class="n">to</span> <span class="n">generate</span> <span class="n">comprehensive</span> <span class="n">fragmentation</span> <span class="n">features</span> <span class="kn">from</span> <span class="nn">large</span> <span class="n">cfDNA</span> <span class="n">genomic</span> <span class="n">sequencing</span> <span class="n">data</span><span class="o">.</span> <span class="n">For</span> <span class="n">instance</span><span class="p">,</span> <span class="n">FinaleToolkit</span> <span class="n">can</span> <span class="n">generate</span> <span class="n">genome</span><span class="o">-</span><span class="n">wide</span> <span class="n">WPS</span> <span class="n">features</span> <span class="kn">from</span> <span class="nn">a</span> \<span class="o">~</span><span class="p">{}</span><span class="mi">100</span><span class="n">X</span> <span class="n">cfDNA</span> <span class="n">whole</span><span class="o">-</span><span class="n">genome</span> <span class="n">sequencing</span> <span class="p">(</span><span class="n">WGS</span><span class="p">)</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="mf">1.2</span> <span class="n">hours</span> <span class="n">using</span> <span class="mi">16</span> <span class="n">CPU</span> <span class="n">cores</span><span class="p">,</span> <span class="n">offering</span> <span class="n">up</span> <span class="n">to</span> <span class="n">a</span> \<span class="o">~</span><span class="p">{}</span><span class="mi">50</span><span class="o">-</span><span class="n">fold</span> <span class="n">increase</span> <span class="ow">in</span> <span class="n">processing</span> <span class="n">speed</span> <span class="n">compared</span> <span class="n">to</span> <span class="n">original</span> <span class="n">implementations</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">same</span> <span class="n">dataset</span><span class="o">.</span> <span class="n">We</span> <span class="n">have</span> <span class="n">benchmarked</span> <span class="n">FinaleToolkit</span> <span class="n">against</span> <span class="n">original</span> <span class="n">studies</span> <span class="ow">or</span> <span class="n">implementations</span> <span class="n">where</span> <span class="n">possible</span><span class="p">,</span> <span class="n">confirming</span> <span class="n">its</span> <span class="n">efficacy</span><span class="o">.</span> <span class="n">Furthermore</span><span class="p">,</span> <span class="n">FinaleToolkit</span> <span class="n">enabled</span> <span class="n">the</span> <span class="n">genome</span><span class="o">-</span><span class="n">wide</span> <span class="n">analysis</span> <span class="n">of</span> <span class="n">fragmentation</span> <span class="n">patterns</span> <span class="n">over</span> <span class="n">arbitrary</span> <span class="n">genomic</span> <span class="n">intervals</span><span class="p">,</span> <span class="n">significantly</span> <span class="n">boosting</span> <span class="n">the</span> <span class="n">performance</span> <span class="k">for</span> <span class="n">cancer</span> <span class="n">early</span> <span class="n">detection</span><span class="o">.</span> <span class="n">FinaleToolkit</span> <span class="ow">is</span> <span class="nb">open</span> <span class="n">source</span> <span class="ow">and</span> <span class="n">thoroughly</span> <span class="n">documented</span> <span class="k">with</span> <span class="n">both</span> <span class="n">command</span> <span class="n">line</span> <span class="n">interface</span> <span class="ow">and</span> <span class="n">Python</span> <span class="n">application</span> <span class="n">programming</span> <span class="n">interface</span> <span class="p">(</span><span class="n">API</span><span class="p">)</span> <span class="n">to</span> <span class="n">facilitate</span> <span class="n">its</span> <span class="n">widespread</span> <span class="n">adoption</span> <span class="ow">and</span> <span class="n">use</span> <span class="n">within</span> <span class="n">the</span> <span class="n">research</span> <span class="n">community</span><span class="p">:</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">epifluidlab</span><span class="o">/</span><span class="n">FinaleToolkitCompeting</span> <span class="n">Interest</span> <span class="n">StatementY</span><span class="o">.</span><span class="n">L</span><span class="o">.</span> <span class="n">owns</span> <span class="n">stocks</span> <span class="kn">from</span> <span class="nn">Freenome</span> <span class="n">Inc</span><span class="o">.</span> <span class="n">The</span> <span class="n">remaining</span> <span class="n">authors</span> <span class="n">declare</span> <span class="n">no</span> <span class="n">competing</span> <span class="n">interests</span><span class="o">.</span><span class="p">},</span>
<span class="n">URL</span> <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">biorxiv</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">content</span><span class="o">/</span><span class="n">early</span><span class="o">/</span><span class="mi">2024</span><span class="o">/</span><span class="mi">06</span><span class="o">/</span><span class="mi">02</span><span class="o">/</span><span class="mf">2024.05.29.596414</span><span class="p">},</span>
<span class="n">eprint</span> <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">biorxiv</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">content</span><span class="o">/</span><span class="n">early</span><span class="o">/</span><span class="mi">2024</span><span class="o">/</span><span class="mi">06</span><span class="o">/</span><span class="mi">02</span><span class="o">/</span><span class="mf">2024.05.29.596414</span><span class="o">.</span><span class="n">full</span><span class="o">.</span><span class="n">pdf</span><span class="p">},</span>
<span class="n">journal</span> <span class="o">=</span> <span class="p">{</span><span class="n">bioRxiv</span><span class="p">}</span>
<span class="p">}</span>
</pre></div>
</div>
</section>
<section id="contact">
<h2>Contact<a class="headerlink" href="#contact" title="Link to this heading">#</a></h2>
<div class="line-block">
<div class="line"><strong>James Wenhan Li</strong></div>
<div class="line">Email: <a class="reference external" href="mailto:lijw21%40wfu.edu">lijw21<span>@</span>wfu<span>.</span>edu</a></div>
</div>
<div class="line-block">
<div class="line"><strong>Ravi Bandaru</strong></div>
<div class="line">Email: <a class="reference external" href="mailto:ravi.bandaru%40northwestern.edu">ravi<span>.</span>bandaru<span>@</span>northwestern<span>.</span>edu</a></div>
</div>
<div class="line-block">
<div class="line"><strong>Yaping Liu</strong></div>
<div class="line">Email: <a class="reference external" href="mailto:yaping%40northwestern.edu">yaping<span>@</span>northwestern<span>.</span>edu</a></div>
</div>
</section>
<section id="license">
<h2>License<a class="headerlink" href="#license" title="Link to this heading">#</a></h2>
<p>Please refer to the <a class="reference external" href="https://github.com/epifluidlab/FinaleToolkit/blob/main/LICENSE">MIT license</a>.</p>
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