Correcting a Single Deletion in Reads from a Nanopore Sequencer
CoRR(2024)
摘要
Owing to its several merits over other DNA sequencing technologies, nanopore
sequencers hold an immense potential to revolutionize the efficiency of DNA
storage systems. However, their higher error rates necessitate further research
to devise practical and efficient coding schemes that would allow accurate
retrieval of the data stored. Our work takes a step in this direction by
adopting a simplified model of the nanopore sequencer inspired by Mao et
al., which incorporates some of its physical aspects. This channel model can
be viewed as a sliding window of length ℓ that passes over the incoming
input sequence and produces the L_1-weight of the enclosed ℓ bits, while
shifting by one position at each time step. The resulting (ℓ+1)-ary
vector, referred to as the ℓ-read vector, is susceptible to
deletion errors due to imperfections inherent in the sequencing process. We
establish that at least log n - ℓ bits of redundancy are needed to
correct a single deletion. An error-correcting code that is optimal up to an
additive constant, is also proposed. Furthermore, we find that for ℓ≥
2, reconstruction from two distinct noisy ℓ-read vectors can be
accomplished without any redundancy, and provide a suitable reconstruction
algorithm to this effect.
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