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dc.contributor.authorHan, Renmin
dc.contributor.authorLi, Yu
dc.contributor.authorGao, Xin
dc.contributor.authorWang, Sheng
dc.date.accessioned2019-02-27T08:25:45Z
dc.date.available2019-02-27T08:25:45Z
dc.date.issued2018-09-08
dc.identifier.citationHan R, Li Y, Gao X, Wang S (2018) An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. Bioinformatics 34: i722–i731. Available: http://dx.doi.org/10.1093/bioinformatics/bty555.
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.doi10.1093/bioinformatics/bty555
dc.identifier.urihttp://hdl.handle.net/10754/631196
dc.description.abstractMotivation Long-reads, point-of-care and polymerase chain reaction-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the end-to-end mapping between the raw electrical current signal sequence and the reference expected signal sequence serves as the key building block to signal labeling, and the following signal visualization, variant identification and methylation detection. One of the classic algorithms to solve the signal mapping problem is the dynamic time warping (DTW). However, the ultra-long nanopore sequencing and an order of magnitude difference in the sampling speed complexify the scenario and make the classical DTW infeasible to solve the problem. Results Here, we propose a novel multi-level DTW algorithm, continuous wavelet DTW (cwDTW), based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can gain remarkable acceleration with tiny loss of the alignment accuracy. On the real nanopore datasets, cwDTW can finish an alignment task in few seconds, which is about 3000 times faster than the original DTW. By successfully applying cwDTW on the tasks of signal labeling and ultra-long sequence comparison, we further demonstrate the power and applicability of cwDTW. Availability and implementation Our program is available at https://github.com/realbigws/cwDTW. Supplementary information Supplementary data are available at Bioinformatics online.
dc.description.sponsorshipThis work was supported by the Kind Abdullah Unviersity of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No. FCC/1/1976-04, URF/1/2601-01, URF/1/3007-01, URF/1/3412-01 and URF/1/3450-01.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/bioinformatics/article/34/17/i722/5093233
dc.rightsThis is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The version of record is available online at: https://academic.oup.com/bioinformatics/article/34/17/i722/5093233.
dc.titleAn accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing
dc.typeArticle
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.identifier.journalBioinformatics
dc.eprint.versionPost-print
kaust.personHan, Renmin
kaust.personLi, Yu
kaust.personGao , Xin
kaust.personWang, Sheng
kaust.grant.numberFCC/1/1976-04
kaust.grant.numberURF/1/2601-01
kaust.grant.numberURF/1/3007-01
kaust.grant.numberURF/1/3412-01
kaust.grant.numberURF/1/3450-01
dc.relation.issupplementedbygithub:realbigws/cwDTW
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Software]</i> <br/> Title: realbigws/cwDTW: Continuous Wavelet Dynamic Time Warping for unbalanced global mapping of two signals. Publication Date: 2017-10-31. github: <a href="https://github.com/realbigws/cwDTW" >realbigws/cwDTW</a> Handle: <a href="http://hdl.handle.net/10754/666986" >10754/666986</a></a></li></ul>
dc.date.published-online2018-09-08
dc.date.published-print2018-09-01


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