Capacity of the Shotgun Sequencing Channel

Aditya Narayan Ravi, Alireza Vahid, Ilan Shomorony

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

Abstract

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in [1], is what read length and coverage depth (i.e., the total number of reads) are needed to guarantee reliable sequence reconstruction. Motivated by DNA-based storage, we study the coded version of this problem; i.e., the scenario in which the DNA molecule being sequenced is a codeword from a predefined codebook. Our main result is an exact characterization of the capacity of the resulting shotgun sequencing channel as a function of the read length and coverage depth. In particular, our results imply that while in the uncoded case, O(n) reads of length greater than 2logn are needed for reliable reconstruction of a length-n binary sequence, in the coded case, only O(n/log n) reads of length greater than log n are needed for the capacity to be arbitrarily close to 1.

Original languageEnglish (US)
Title of host publication2022 IEEE International Symposium on Information Theory, ISIT 2022
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages210-215
Number of pages6
ISBN (Electronic)9781665421591
DOIs
StatePublished - 2022
Event2022 IEEE International Symposium on Information Theory, ISIT 2022 - Espoo, Finland
Duration: Jun 26 2022Jul 1 2022

Publication series

NameIEEE International Symposium on Information Theory - Proceedings
Volume2022-June
ISSN (Print)2157-8095

Conference

Conference2022 IEEE International Symposium on Information Theory, ISIT 2022
Country/TerritoryFinland
CityEspoo
Period6/26/227/1/22

Keywords

  • DNA shotgun sequencing
  • DNA-based storage
  • channel capacity

ASJC Scopus subject areas

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

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