Coded Shotgun Sequencing

Ravi, Aditya Narayan; Vahid, Alireza; Shomorony, Ilan

doi:10.48550/arxiv.2110.02868

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2022

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“…Rapid advances in DNA-based storage with today's technology attract a significant amount of research attention from an information-theoretic perspective where DNA-based storage acts as a communication channel [4,5,[14][15][16][17][18]. Among these, [17,18] use coding over a set of short sequences that are randomly sequenced and then shuffled in an unordered fashion.…”

Section: A Related Workmentioning

confidence: 99%

Reassembly Codes for the Chop-and-Shuffle Channel

Nassirpour¹,

Shomorony²,

Vahid³

2022

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We study the problem of retrieving data from a channel that breaks the input sequence into a set of unordered fragments of random lengths, which we refer to as the chop-and-shuffle channel. The length of each fragment follows a geometric distribution. We propose nested Varshamov-Tenengolts (VT) codes to recover the data. We evaluate the error rate and the complexity of our scheme numerically. Our results show that the decoding error decreases as the input length increases, and our method has a significantly lower complexity than the baseline brute-force approach. We also propose a new construction for VT codes, quantify the maximum number of the required parity bits, and show that our approach requires fewer parity bits compared to known results.

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