1<!DOCTYPE html> 2<html> 3 4 <head> 5 <meta charset="utf-8"> 6 <meta http-equiv="X-UA-Compatible" content="IE=edge"> 7 <meta name="viewport" content="width=device-width, initial-scale=1"> 8 <title>Cheng Lab - Research & Software</title> 9 <meta name="description" content="Cheng Lab -- Research & Software"> 10 <link rel="stylesheet" href="/css/main.css"> 11 <link rel="canonical" href="/research/"> 12 13
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23 24 25 26</head> 27 28 29 <body> 30 31 <div class="navbar navbar-default navbar-fixed-top" role="navigation"> 32 <div class="container-fluid"> 33 <div class="navbar-header"> 34 <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar-collapse-1" aria-expanded="false"> 35 <span class="sr-only">Toggle navigation</span> 36 <span class="icon-bar"></span> 37 <span class="icon-bar"></span> 38 <span class="icon-bar"></span> 39 </button> 40 41 <a class="navbar-brand" href="/">Cheng Lab @ Yale BIDS</a> 42 </div> 43 <div class="collapse navbar-collapse" id="navbar-collapse-1"> 44 <ul class="nav navbar-nav navbar-right"> 45 <li><a href="/">Home</a></li> 46 <li><a href="/team">Team</a></li> 47 <li><a href="/vacancies">Vacancies</a></li> 48 <li><a href="/publications">Publications</a></li> 49 <li><a href="/research">Research & Software</a></li> 50 <!-- li><a href="/pictures">(Pics)</a></li> --> 51 </ul> 52 </div> 53 </div> 54</div> 55 56 57 <div class="container-fluid"> 58 <div class="row"> 59 <div id="textid" class="col-sm-12"> 60 <h1 id="research">Research</h1> 61 62<p>Our overarching goal is to develop novel algorithms to address important and fundamental problems in computational genomics. Below are some of the key research themes we are currently exploring:</p> 63 64<h4 id="high-performance-genome-assembly-algorithm"><strong>High-performance genome assembly algorithm</strong></h4> 65<p><em>De novo</em> assembly, especially <em>de novo</em> haplotype-resolved assembly, has been a central problem and remains one of the most challenging tasks in bioinformatics for four decades. It involves multiple advanced algorithms such as sketching, alignment and many branches in graph theory, and demands programming skills of the highest level. We have developed a series of <em>de novo</em> assembly algorithms, including hifiasm, hifiasm (Hi-C) and hifiasm (UL), which are designed to produce optimal genome assemblies by combining different data types. These algorithms have been widely used and have already become the dominant long-read genome assemblers. Currently, we are particularly interested in developing <em>de novo</em> assembly algorithms for complex genomes with polyploid alterations such as cancer genomes and polyploid plant genomes.</p> 66 67<h4 id="comprehensive-variant-calling-and-interpretation"><strong>Comprehensive variant calling and interpretation</strong></h4> 68<p>For the human genome, variant calling is typically performed through read alignment, which aligns fragmented reads back to the human reference genome. However, the generic reference genome often lacks specific personal information, leading to potential inaccuracies and biases, especially within highly repetitive and structurally different regions. Consequently, there is a rapidly growing demand for <em>de novo</em> genome assemblyâa methodology that reconstructs the genome without relying on a reference. Leveraging our computational expertise, we aim to develop innovative variant calling and interpretation methods that are based on <em>de novo</em> genome assembly.</p> 69 70<h4 id="resolving-challenging-medically-relevant-genes"><strong>Resolving challenging medically relevant genes</strong></h4> 71<p>Many critical medically relevant genes, such as HLA, SMN1, SMN2, C3, C4, and NOTCH2NLC, are difficult to resolve 72due to high repetitiveness and structural variation. Most computational approaches rely on read-to-reference 73alignments, which are constrained by the inaccuracies in reference genomes. Our goal is to develop assembly-based, 74reference-free computational methods to accurately reconstruct these challenging genomic regions.</p> 75 76<h1 id="software">Software</h1> 77 78<ul> 79 <li><a href="https://github.com/chhylp123/hifiasm">hifiasm</a>: a comprehensive <em>de novo</em> genome assembly toolkit supporting various data types and functionalities, 80published in <a href="https://www.nature.com/articles/s41592-020-01056-5">Cheng et al (2021)</a>, <a href="https://www.nature.com/articles/s41587-022-01261-x">Cheng et al (2022)</a>, <a href="https://www.nature.com/articles/s41592-024-02269-8">Cheng et al (2024)</a>
80 and <a href="https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1">Cheng et al (2025)</a>. 81<img style="margin: 0px" src="https://img.shields.io/github/stars/chhylp123/hifiasm" /> 82<a href="https://bioconda.github.io/recipes/hifiasm/README.html"><img style="margin: 0px" src="https://img.shields.io/conda/dn/bioconda/hifiasm.svg?style=flag&label=Bioconda" /></a></li> 83</ul> 84 85 86</div> 87 88 </div> 89 </div> 90 91 <div id="footer" class="panel"> 92 <div class="panel-footer"> 93 <div class="container-fluid"> 94 <div class="row"> 95 <div class="col-sm-4"> 96 97 <p>Site made with <a href="https://jekyllrb.com">Jekyll</a> based on source code from the <a href="https://hlilab.github.io/">Allan Lab</a> </p> 98 99 100 101 <p> </p><p> 102 103 104 </div> 105 <div class="col-sm-4"> 106 <p>We are part of the <a href="https://medicine.yale.edu/biomedical-informatics-data-science/">Department of Biomedical Informatics and Data Science</a> at the<a href="https://medicine.yale.edu/"> Yale School of Medicine</a>.</p> 107 </div> 108 <div class="col-sm-4"> 109 Contact: 101 College Street, Fl 10<br /> 110 New Haven, Connecticut 06510<br /> 111 </div> 112 </div> 113 </div> 114 </div> 115</div> 116
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