OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach
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AbstractMotivation: 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.
All Author(s) ListAlden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok Kevin Y. Yip, Ting-Fung Chan
Journal nameBioinformatics
Year2016
Month9
Day30
Volume Number33
Issue Number3
PublisherOxford University Press
Pages311 - 319
ISSN1367-4803
eISSN1460-2059
LanguagesEnglish-United Kingdom

Last updated on 2020-05-08 at 01:37