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

arXiv2107.06440MaRDI QIDQ6372736FDOQ6372736

Authors: Sundara Rajan Srinivasavaradhan, Sivakanth Gopi, Henry D. Pfister, Sergey Yekhanin 

Publication date: 13 July 2021

Abstract: 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 the 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 a new dataset of traces that will be publicly released with the paper. Our hope is that this dataset will enable research progress by allowing objective comparisons between candidate algorithms.

Has companion code repository: https://github.com/microsoft/clustered-nanopore-reads-dataset

This page was built for publication: Trellis BMA: Coded Trace Reconstruction on IDS Channels for DNA Storage

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q6372736)