Sequence assembly from corrupted shotgun reads

Shirshendu Ganguly, Elchanan Mossel, Miklos Z. Racz

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

2 Scopus citations

Abstract

The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to reconstruct the original sequence. There are many different technologies that generate the reads: widely-used second-generation methods create short reads with low error rates, while emerging third-generation methods create long reads with high error rates. Both error rates and error profiles differ among methods, so reconstruction algorithms are often tailored to specific shotgun sequencing technologies. As these methods change over time, a fundamental question is whether there exist reconstruction algorithms which are robust, i.e., which perform well under a wide range of error distributions. Here we study this question of sequence assembly from corrupted reads. We make no assumption on the types of errors in the reads, but only assume a bound on their magnitude. More precisely, for each read we assume that instead of receiving the true read with no errors, we receive a corrupted read which has edit distance at most ϵ times the length of the read from the true read. We show that if the reads are long enough and there are sufficiently many of them, then approximate reconstruction is possible: we construct a simple algorithm such that for almost all original sequences the output of the algorithm is a sequence whose edit distance from the original one is at most O(ϵ) times the length of the original sequence.

Original languageEnglish (US)
Title of host publicationProceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages265-269
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

All Science Journal Classification (ASJC) codes

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

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    Ganguly, S., Mossel, E., & Racz, M. Z. (2016). Sequence assembly from corrupted shotgun reads. In Proceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory (pp. 265-269). [7541302] (IEEE International Symposium on Information Theory - Proceedings; Vol. 2016-August). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2016.7541302