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Sequencing a DNA strand, as part of the read process in DNA storage, producesmultiple noisy copies which can be combined to produce better estimates of theoriginal strand; this is called trace reconstruction. One can reduce the errorrate further by introducing redundancy in the write sequence and this is calledcoded trace reconstruction. In this paper, we model the DNA storage channel asan insertion-deletion-substitution (IDS) channel and design both encodingschemes and low-complexity decoding algorithms for coded trace reconstruction.  We introduce Trellis BMA, a new reconstruction algorithm whose complexity islinear in the number of traces, and compare its performance to previousalgorithms. Our results show that it reduces the error rate on both simulatedand experimental data. The performance comparisons in this paper are based on anew dataset of traces that will be publicly released with the paper. Our hopeis that this dataset will enable research progress by allowing objectivecomparisons between candidate algorithms.

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