Finite-state semi-Markov channels for nanopore sequencing

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Abstract

Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol interference, and noisy measurements by concatenating an i.i.d. duplication channel with a finite-state semi-Markov channel. Compared to previous models, this channel models the dominant distortions of the nanopore while remaining tractable. Anticipating future coding schemes, we derive MAP detection algorithms and estimate achievable rates. Given that finite-state semi-Markov channels are a subclass of channels with memory, we conjecture that the achievable rate of the noisy nanopore channel can be optimised using a variation of the generalised Blahut-Arimoto algorithm.

Original languageEnglish
Title of host publication2022 IEEE International Symposium on Information Theory, ISIT 2022
EditorsMuriel Médard, Mikael Skoglund, Aylin Yener
Place of PublicationPiscataway NJ USA
PublisherIEEE, Institute of Electrical and Electronics Engineers
Pages216-221
Number of pages6
ISBN (Electronic)9781665421591
ISBN (Print)9781665421607
DOIs
Publication statusPublished - 2022
EventIEEE International Symposium on Information Theory 2022 - Espoo, Finland
Duration: 26 Jun 20221 Jul 2022
https://ieeexplore.ieee.org/xpl/conhome/9834325/proceeding (Proceedings)
https://www.isit2022.org/ (Website)

Publication series

NameIEEE International Symposium on Information Theory - Proceedings
PublisherIEEE, Institute of Electrical and Electronics Engineers
Volume2022-June
ISSN (Print)2157-8095
ISSN (Electronic)2157-8117

Conference

ConferenceIEEE International Symposium on Information Theory 2022
Abbreviated titleISIT 2022
Country/TerritoryFinland
CityEspoo
Period26/06/221/07/22
Internet address

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