High accuracy base calls in nanopore sequencing

Philippe Faucon, Robert Trevino, Parithi Balachandran, Kylie Standage-Beier, Xiao Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Nanopore sequencing has introduced the ability to sequence long stretches of DNA, enabling the resolution of repeating segments, or paired SNPs across long stretches of DNA. Unfortunately, significant error rates >15%, introduced through systematic and random noise inhibit downstream analysis. We propose a novel method, using unsupervised learning, to correct biologically amplified reads before downstream analysis proceeds. We also demonstrate that our method has performance comparable to existing techniques without limiting the detection of repeats, or the length of the input sequence.

Original languageEnglish (US)
Title of host publicationProceedings of 2017 6th International Conference on Bioinformatics and Biomedical Science, ICBBS 2017
PublisherAssociation for Computing Machinery
Pages12-16
Number of pages5
VolumePart F130950
ISBN (Electronic)9781450352222
DOIs
Publication statusPublished - Jun 22 2017
Externally publishedYes
Event6th International Conference on Bioinformatics and Biomedical Science, ICBBS 2017 - Singapore, Singapore
Duration: Jun 22 2017Jun 24 2017

Other

Other6th International Conference on Bioinformatics and Biomedical Science, ICBBS 2017
CountrySingapore
CitySingapore
Period6/22/176/24/17

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Keywords

  • Accuracy improvement
  • DNA thumbprint
  • Nanopore sequencing

ASJC Scopus subject areas

  • Human-Computer Interaction
  • Computer Networks and Communications
  • Computer Vision and Pattern Recognition
  • Software

Cite this

Faucon, P., Trevino, R., Balachandran, P., Standage-Beier, K., & Wang, X. (2017). High accuracy base calls in nanopore sequencing. In Proceedings of 2017 6th International Conference on Bioinformatics and Biomedical Science, ICBBS 2017 (Vol. Part F130950, pp. 12-16). Association for Computing Machinery. https://doi.org/10.1145/3121138.3121186