Overlap-based genome assembly from variable-length reads

Joseph Hui, Ilan Shomorony, Kannan Ramchandran, Thomas A. Courtade

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

Abstract

Recently developed high-throughput sequencing platforms can generate very long reads, making the perfect assembly of whole genomes information-theoretically possible [1]. One of the challenges in achieving this goal in practice, however, is that traditional assembly algorithms based on the de Bruijn graph framework cannot handle the high error rates of long-read technologies. On the other hand, overlap-based approaches such as string graphs [2] are very robust to errors, but cannot achieve the theoretical lower bounds. In particular, these methods handle the variable-length reads provided by long-read technologies in a suboptimal manner. In this work, we introduce a new assembly algorithm with two desirable features in the context of long-read sequencing: (1) it is an overlap-based method, thus being more resilient to read errors than de Bruijn graph approaches; and (2) it achieves the information-theoretic bounds even in the variable-length read setting.

Original languageEnglish (US)
Title of host publicationProceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1018-1022
Number of pages5
ISBN (Electronic)9781509018062
DOIs
StatePublished - Aug 10 2016
Externally publishedYes
Event2016 IEEE International Symposium on Information Theory, ISIT 2016 - Barcelona, Spain
Duration: Jul 10 2016Jul 15 2016

Publication series

NameIEEE International Symposium on Information Theory - Proceedings
Volume2016-August
ISSN (Print)2157-8095

Other

Other2016 IEEE International Symposium on Information Theory, ISIT 2016
CountrySpain
CityBarcelona
Period7/10/167/15/16

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Information Systems
  • Modeling and Simulation
  • Applied Mathematics

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