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

TL;DR

This paper introduces Trellis BMA, a low-complexity algorithm for coded trace reconstruction in DNA storage, modeled as an IDS channel, demonstrating improved error rates on simulated and real data.

Contribution

The paper presents a novel Trellis BMA algorithm for coded trace reconstruction with linear complexity, tailored for IDS channels in DNA storage.

Findings

Reduces error rate on simulated data

Improves performance on experimental data

Provides a new dataset for benchmarking algorithms

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.