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 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.

Automated summary

In this paper, a new reconstruction algorithm named Trellis BMA is introduced for coded trace reconstruction, with complexity linear in the number of traces, showing reduced error rates in simulated and experimental data. Encoding schemes and low-complexity decoding algorithms are designed for DNA storage modeled as an IDS channel, aiming to facilitate research progress through objective comparisons using the publicly released Clustered Nanopore Reads Dataset.