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dc.contributor.authorHan, Renmin
dc.contributor.authorWang, Sheng
dc.contributor.authorGao, Xin
dc.date.accessioned2019-10-16T07:38:54Z
dc.date.available2019-10-16T07:38:54Z
dc.date.issued2019-10-08
dc.identifier.citationHan, R., Wang, S., & Gao, X. (2019). Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. Bioinformatics. doi:10.1093/bioinformatics/btz742
dc.identifier.doi10.1093/bioinformatics/btz742
dc.identifier.urihttp://hdl.handle.net/10754/658636
dc.description.abstractMOTIVATION:Genome diagnostics have gradually become a prevailing routine for human healthcare. With the advances in understanding the causal genes for many human diseases, targeted sequencing provides a rapid, cost-efficient and focused option for clinical applications, such as SNP detection and haplotype classification, in a specific genomic region. Although nanopore sequencing offers a perfect tool for targeted sequencing because of its mobility, PCR-freeness, and long read properties, it poses a challenging computational problem of how to efficiently and accurately search and map genomic subsequences of interest in a pool of nanopore reads (or raw signals). Due to its relatively low sequencing accuracy, there is no reliable solution to this problem, especially at low sequencing coverage. RESULTS:Here, we propose a brand new signal-based subsequence inquiry pipeline as well as two novel algorithms to tackle this problem. The proposed algorithms follow the principle of subsequence dynamic time warping and directly operate on the electrical current signals, without loss of information in base-calling. Therefore, the proposed algorithms can serve as a tool for sequence inquiry in targeted sequencing. Two novel criteria are offered for the consequent signal quality analysis and data classification. Comprehensive experiments on real-world nanopore datasets show the efficiency and effectiveness of the proposed algorithms. We further demonstrate the potential applications of the proposed algorithms in two typical tasks in nanopore-based targeted sequencing: SNP detection under low sequencing coverage, and haplotype classification under low sequencing accuracy. AVAILABILITY:The project is accessible at https://github.com/icthrm/cwSDTWnano.git, and the presented bench data is available upon request.
dc.description.sponsorshipThe authors thank Minh Duc Cao, Lachlan J.M. Coin, Louise Roddam and Tania Duarte for providing the nanopore sequencing data. This work was supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No. FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, URF/1/3412-01-01, and URF/1/3450-01-01.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz742/5583772
dc.rightsThis is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics (Oxford, England) following peer review. The version of record is available online at: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz742/5583772.
dc.titleNovel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted 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 (Oxford, England)
dc.rights.embargodate2020-10-09
dc.eprint.versionPost-print
kaust.personHan, Renmin
kaust.personWang, Sheng
kaust.personGao, Xin
kaust.grant.numberFCC/1/1976-18-01
kaust.grant.numberFCC/1/1976-23-01
kaust.grant.numberFCC/1/1976-25-01
kaust.grant.numberFCC/1/1976-26-01
kaust.grant.numberURF/1/3412-01
kaust.grant.numberURF/1/3450-01-01
dc.relation.issupplementedbygithub:icthrm/cwSDTWnano
refterms.dateFOA2020-10-09T00:00:00Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Software]</i> <br/> Title: icthrm/cwSDTWnano. Publication Date: 2018-10-28. github: <a href="https://github.com/icthrm/cwSDTWnano" >icthrm/cwSDTWnano</a> Handle: <a href="http://hdl.handle.net/10754/667008" >10754/667008</a></a></li></ul>
kaust.acknowledged.supportUnitOffice of Sponsored Research (OSR)


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