He Cheng, Lin Guifang, Wei Hairong, Tang Haibao, White Frank F, Valent Barbara, Liu Sanzhen
Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS 66506-5502, USA.
College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
NAR Genom Bioinform. 2020 Sep 21;2(3):lqaa075. doi: 10.1093/nargab/lqaa075. eCollection 2020 Sep.
Genome sequences provide genomic maps with a single-base resolution for exploring genetic contents. Sequencing technologies, particularly long reads, have revolutionized genome assemblies for producing highly continuous genome sequences. However, current long-read sequencing technologies generate inaccurate reads that contain many errors. Some errors are retained in assembled sequences, which are typically not completely corrected by using either long reads or more accurate short reads. The issue commonly exists, but few tools are dedicated for computing error rates or determining error locations. In this study, we developed a novel approach, referred to as -mer abundance difference (KAD), to compare the inferred copy number of each -mer indicated by short reads and the observed copy number in the assembly. Simple KAD metrics enable to classify -mers into categories that reflect the quality of the assembly. Specifically, the KAD method can be used to identify base errors and estimate the overall error rate. In addition, sequence insertion and deletion as well as sequence redundancy can also be detected. Collectively, KAD is valuable for quality evaluation of genome assemblies and, potentially, provides a diagnostic tool to aid in precise error correction. KAD software has been developed to facilitate public uses.
基因组序列提供了具有单碱基分辨率的基因组图谱，用于探索遗传内容。测序技术，特别是长读长测序技术，已经彻底改变了基因组组装方式，能够产生高度连续的基因组序列。然而，当前的长读长测序技术会产生包含许多错误的不准确读数。一些错误会保留在组装序列中，通常无论是使用长读长还是更准确的短读长都无法完全校正这些错误。这个问题普遍存在，但专门用于计算错误率或确定错误位置的工具却很少。在本研究中，我们开发了一种新方法，称为k-mer丰度差异（KAD），用于比较短读长所指示的每个k-mer的推断拷贝数与组装体中观察到的拷贝数。简单的KAD指标能够将k-mer分类为反映组装质量的类别。具体而言，KAD方法可用于识别碱基错误并估计总体错误率。此外，还可以检测序列插入、缺失以及序列冗余。总体而言，KAD对于基因组组装的质量评估很有价值，并且有可能提供一种诊断工具来辅助精确的错误校正。目前已经开发了KAD软件以方便公众使用。
