Merge branch 'main' of https://github.com/Kuanhao-Chao/LiftOn into main

README.md

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 <div class="content">
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 LiftOn is a homology-based lift-over tool using both DNA-DNA alignments (from <a href="https://academic.oup.com/bioinformatics/article/37/12/1639/6035128?login=true" target="_blank">Liftoff</a>, credits to <a href="https://scholar.google.com/citations?user=N3tXk7QAAAAJ&amp;hl=en" target="_blank">Dr. Alaina Shumate</a>) and protein-DNA alignments (from <a href="https://academic.oup.com/bioinformatics/article/39/1/btad014/6989621" target="_blank">miniprot</a>, credits to <a href="http://liheng.org" target="_blank">Dr. Heng Li</a>) to accurately map annotations between genome assemblies of the same or different species. LiftOn employs a two-step <a href="https://ccb.jhu.edu/lifton/content/behind_scenes.html#protein-maximization-algorithm">protein maximization algorithm</a> to improve the annotation of protein-coding genes in the T2T-CHM13 <a href="https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz" target="_blank">JHU RefSeqv110 + Liftoff v5.1</a> annotation.
-The latest T2T-CHM13 annotation generated by LiftOn is available as <a href="https://tinyurl.com/4xywtwve" target="_blank">JHU_LiftOn_v1.0_chm13v2.0.gff3 (ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/JHU_LiftOn_v1.0_chm13v2.0.gff3) <i class="fa fa-download"></i></a>.<section id="why-lifton" class="">
+The latest T2T-CHM13 annotation generated by LiftOn is available as <a href="https://tinyurl.com/4xywtwve" target="_blank">JHU_LiftOn_v1.0_chm13v2.0.gff3 (ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/JHU_LiftOn_v1.0_chm13v2.0.gff3) <i class="fa fa-download"></i></a>.
+
+<section id="installation-wrap" class="">
+<h2>Installation<a class="headerlink" href="#installation-wrap" title="Permalink to this heading">#</a></h2>
+
+<section id="install-through-pip">
+<span id="id2"></span><h3>Install through pip<a class="headerlink" href="#install-through-pip" title="Permalink to this heading">#</a></h3>
+<p>LiftOn is on <a class="reference external" href="https://pypi.org/project/lifton/">PyPi</a> now. Check out all the releases <a class="reference external" href="https://pypi.org/manage/project/lifton/releases/">here</a>. Pip automatically resolves and installs any dependencies required by LiftOn.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ pip install lifton
+</pre></div>
+</div>
+<div class="line-block">
+</div>
+</section>
+
+<section id="install-from-source">
+<span id="id4"></span><h3>Install from source<a class="headerlink" href="#install-from-source" title="Permalink to this heading">#</a></h3>
+<p>You can also install LiftOn from source. Check out the <a class="reference external" href="https://github.com/Kuanhao-Chao/LiftOn">latest version </a>
+!</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ git clone https://github.com/Kuanhao-Chao/LiftOn
+
+$ python setup.py install
+</pre></div>
+</div>
+<div class="line-block">
+<div class="line"><br></div>
+</div>
+</section>
+</section>
+
+
+<section id="why-lifton" class="">
 <h2>Why LiftOn❓<a class="headerlink" href="#why-lifton" title="Permalink to this heading">#</a></h2>
 <ol class="arabic simple">
 <li><p><strong>Burgeoning number of genome assemblies</strong>: As of December 2023, there are 30,530 eukaryotic genomes, 567,228 prokaryotic genomes, and 66,429 viruses listed on NCBI (<a class="reference external" href="https://www.ncbi.nlm.nih.gov/genome/browse/#!/overview/">NCBI genome browser</a>). However, genome annotation is lagging behind. As more high-quality assemblies are generated, we need an accurate lift-over tool to annotate them.</p></li>