WE1.R6.2

Code Design for Duplex Read Sequencing

Adrian Vidal, Viduranga Bandara Wijekoon, Emanuele Viterbo, Monash University, Australia

Session:
Coding in Biology 3

Track:
17: Information and Coding in Biology

Location:
Sigma/Delta

Presentation Time:
Wed, 10 Jul, 10:10 - 10:30

Session Chair:
Emanuele Viterbo, Monash University
Abstract
THIS PAPER IS ELIGIBLE FOR THE STUDENT PAPER AWARD. Motivated by duplex read sequencing developed by Oxford Nanopore Technologies, this paper proposes a concatenated coding scheme for nanopore sequencers where DNA sequences are decoded from noisy reads of the template and reverse-complement strands from the same DNA molecule, that is, a duplex read. First, we show that the double-strand pairwise error probability (PEP) bound is multiplicative with respect to the single-strand PEP bounds of the template and reverse-complement codebooks, thus giving duplex decoders significantly lower error rates compared to simplex decoders which only use the template strand. Then, we propose a decoder for multiple concatenations of short codebooks designed using the double-strand PEP bound.
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