Telomere-to-telomere assembly by preserving contained reads

IF 6.2 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Genome research Pub Date : 2024-10-15 DOI:10.1101/gr.279311.124
Sudhanva Shyam Kamath, Mehak Bindra, Debnath Pal, Chirag Jain
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Abstract

Automated telomere-to-telomere (T2T) de novo assembly of diploid and polyploid genomes remains a formidable task. A string graph is a commonly used assembly graph representation in the assembly algorithms. The string graph formulation employs graph simplification heuristics, which drastically reduce the count of vertices and edges. One of these heuristics involves removing the reads contained in longer reads. In practice, this heuristic occasionally introduces gaps in the assembly by removing all reads that cover one or more genome intervals. The factors contributing to such gaps remain poorly understood. In this work, we mathematically derived the frequency of observing a gap near a germline and a somatic heterozygous variant locus. Our analysis shows that (i) an assembly gap due to contained read deletion is an order of magnitude more frequent in Oxford Nanopore reads than PacBio HiFi reads due to differences in their read-length distributions, and (ii) this frequency decreases with an increase in the sequencing depth. Drawing cues from these observations, we addressed the weakness of the string graph formulation by developing the RAFT assembly algorithm. RAFT addresses the issue of contained reads by fragmenting reads and producing a more uniform read-length distribution. The algorithm retains spanned repeats in the reads during the fragmentation. We empirically demonstrate that RAFT significantly reduces the number of gaps using simulated datasets. Using real Oxford Nanopore and PacBio HiFi datasets of the HG002 human genome, we achieved a twofold increase in the contig NG50 and the number of haplotype-resolved T2T contigs compared to Hifiasm.
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通过保留所含读数进行端粒到端粒组装
二倍体和多倍体基因组的端粒到端粒(T2T)自动从头组装仍然是一项艰巨的任务。字符串图是组装算法中常用的组装图表示法。字符串图表述采用了图简化启发式方法,可大幅减少顶点和边的数量。其中一种启发式方法是删除长读取中包含的读取。在实践中,这种启发式偶尔会在装配中引入间隙,因为它会移除覆盖一个或多个基因组区间的所有读数。造成这种间隙的因素仍然鲜为人知。在这项工作中,我们用数学方法推导了在种系和体细胞杂合变异位点附近观察到间隙的频率。我们的分析表明:(i) 由于牛津纳米孔读数与 PacBio HiFi 读数在读数长度分布上的差异,在牛津纳米孔读数中因包含的读数缺失而导致的装配间隙要比在 PacBio HiFi 读数中出现的频率高出一个数量级;(ii) 随着测序深度的增加,出现间隙的频率会降低。根据这些观察结果,我们开发了 RAFT 组装算法,以解决字符串图公式的弱点。RAFT 通过对读数进行片段化处理,使读数长度分布更加均匀,从而解决了包含读数的问题。该算法在分片过程中保留了读数中的跨距重复序列。我们利用模拟数据集实证证明,RAFT 能显著减少间隙的数量。使用 HG002 人类基因组的真实 Oxford Nanopore 和 PacBio HiFi 数据集,与 Hifiasm 相比,我们的等位基因 NG50 和单体型解析 T2T 等位基因数量增加了两倍。
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来源期刊
Genome research
Genome research 生物-生化与分子生物学
CiteScore
12.40
自引率
1.40%
发文量
140
审稿时长
6 months
期刊介绍: Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.
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