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Channel Model with Memory for DNA Data Storage with Nanopore Sequencing

Belaid Hamoum 1 Elsa Dupraz 2, 1 Laura Conde-Canencia 1 Dominique Lavenier 3
1 Lab-STICC_CODES - Equipe CODES
Lab-STICC - Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance : UMR6285
3 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : This paper is dedicated to channel modeling and error-correction coding for DNA data storage with nanopore sequencing. We first propose a novel statistical model for DNA storage, which takes into account the memory within DNA storage error events, and follows the way nanopore sequencing works. Compared to existing channel models, the proposed model represents more accurate experimental datasets. We also propose a full error-correction scheme for DNA storage, based on a consensus algorithm and non-binary LDPC codes. Especially, we introduce a novel synchronization method which allows to eliminate remaining deletion errors after the consensus, before applying a belief-propagation LDPC decoding algorithm to correct substitution errors. This method exploits the LDPC code structure to correct deletions, and does not require adding any extra redundancy.
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Conference papers
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https://hal-imt-atlantique.archives-ouvertes.fr/hal-03337117
Contributor : Elsa Dupraz <>
Submitted on : Tuesday, September 7, 2021 - 3:56:58 PM
Last modification on : Saturday, September 11, 2021 - 3:44:10 AM

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  • HAL Id : hal-03337117, version 1

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Belaid Hamoum, Elsa Dupraz, Laura Conde-Canencia, Dominique Lavenier. Channel Model with Memory for DNA Data Storage with Nanopore Sequencing. ISTC 2021 - 11th International Symposium on Topics in Coding, Aug 2021, Montreal, Canada. pp.1-5. ⟨hal-03337117⟩

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