OMMA Enables Population-scale Analysis of Complex Genomic Features and Phylogenomic Relationships from Nanochannel-based Optical Maps
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摘要Background: Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples. Findings: We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains. Conclusions: With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.
出版社接受日期17.06.2019
著者Alden King-Yung Leung, Melissa Chun-Jiao Liu, Le Li, Yvonne Yuk-Yin Lai, Catherine Chu, Pui-Yan Kwok, Pak-Leung Ho, Kevin Y Yip, Ting-Fung Chan
期刊名稱GigaScience
出版年份2019
月份7
卷號8
期次7
出版社Oxford University Press (OUP): GigaScience / Oxford University Press
文章號碼giz079
國際標準期刊號2047-217X
語言美式英語

上次更新時間 2020-23-10 於 02:33