Trellis BMA: Coded Trace Reconstruction on IDS Channels for DNA Storage

Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate further by introducing redundancy in write sequence and thi...

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Bibliographic Details
Published in2021 IEEE International Symposium on Information Theory (ISIT) pp. 2453 - 2458
Main Authors Srinivasavaradhan, Sundara Rajan, Gopi, Sivakanth, Pfister, Henry D., Yekhanin, Sergey
Format Conference Proceeding
LanguageEnglish
Published IEEE 12.07.2021
Subjects
Clustering algorithms
DNA
Encoding
Error analysis
Reconstruction algorithms
Redundancy
Sequential analysis
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Summary:Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate further by introducing redundancy in write sequence and this is called coded trace reconstruction. In this paper, we model the DNA storage channel as an insertion-deletion-substitution (IDS) channel and design both encoding schemes and low-complexity decoding algorithms for coded trace reconstruction. We introduce Trellis BMA, a new reconstruction algorithm whose complexity is linear in the number of traces, and compare its performance to previous algorithms. Our results show that it reduces the error rate on both simulated and experimental data. The performance comparisons in this paper are based on the Clustered Nanopore Reads Dataset publicly released with this paper. Our hope is that this dataset will enable research progress by allowing objective comparisons between candidate algorithms.
DOI:10.1109/ISIT45174.2021.9517821