Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing.

Renmin Han, Sheng Wang, Xin Gao

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


MOTIVATION: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, and the presented bench data is available upon request.
Original languageEnglish (US)
Pages (from-to)1333-1343
Number of pages11
JournalBioinformatics (Oxford, England)
Issue number5
StatePublished - Oct 8 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, URF/1/3412-01, URF/1/3450-01-01
Acknowledgements: The 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.


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