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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.
We propose an enhanced version of trellis coded multiple access (TCMA), an overloaded multiple access scheme that outperforms the original TCMA in terms of achieved spectral efficiency. Enhanced TCMA (ETCMA) performs simultaneous transmission of mult
In this paper, code pairs based on trellis coded modulation are proposed over PSK signal sets for a two-user Gaussian multiple access channel. In order to provide unique decodability property to the receiver and to maximally enlarge the constellation
Sparse intersymbol-interference (ISI) channels are encountered in a variety of high-data-rate communication systems. Such channels have a large channel memory length, but only a small number of significant channel coefficients. In this paper, trellis
Let G be a finite strongly connected aperiodic directed graph in which each edge carries a label from a finite alphabet A. Then G induces a trellis coded quantizer for encoding an alphabet A memoryless source. A source sequence of long finite length
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in particular,