OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach
Publication in refereed journal


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摘要Motivation: Optical mapping is a technique for capturing fluorescent signal patterns of long DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping.

Results: Experiments with both synthetic and our real data demonstrate that OMBlast has higher accuracy and faster mapping speed than existing alignment methods. Our tool also shows significant improvement when aligning data with SVs.

Availability and Implementation: OMBlast is implemented for Java 1.7 and is released under a GPL license. OMBlast can be downloaded from https://github.com/aldenleung/OMBlast and run directly on machines equipped with a Java virtual machine.
著者Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok Kevin Y. Yip, Ting-Fung Chan
期刊名稱Bioinformatics
出版年份2016
月份9
日期30
卷號33
期次3
出版社Oxford University Press
頁次311 - 319
國際標準期刊號1367-4803
電子國際標準期刊號1460-2059
語言英式英語

上次更新時間 2021-03-03 於 01:53