The Random Variables of the DNA Coverage Depth Problem
Fuente:
arXiv
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| Autori principali: | , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866918105571131392 |
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| author | Bodur, Şeyma Lia, Stefano López, Hiram H. Ludhani, Rati Ravagnani, Alberto Seccia, Lisa |
| author_facet | Bodur, Şeyma Lia, Stefano López, Hiram H. Ludhani, Rati Ravagnani, Alberto Seccia, Lisa |
| contents | DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on minimizing the expected number of reads needed to recover information strands encoded via a linear code. We compute the asymptotic performance of a recently proposed code construction, establishing and refining a conjecture in the field by giving two independent proofs. We also analyze a geometric code construction based on balanced quasi-arcs and optimize its parameters. Finally, we investigate the full distribution of the random variables that arise in the coverage depth problem, of which the traditionally studied expectation is just the first moment. This allows us to distinguish between code constructions that, at first glance, may appear to behave identically. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2507_20645 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | The Random Variables of the DNA Coverage Depth Problem Bodur, Şeyma Lia, Stefano López, Hiram H. Ludhani, Rati Ravagnani, Alberto Seccia, Lisa Information Theory DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on minimizing the expected number of reads needed to recover information strands encoded via a linear code. We compute the asymptotic performance of a recently proposed code construction, establishing and refining a conjecture in the field by giving two independent proofs. We also analyze a geometric code construction based on balanced quasi-arcs and optimize its parameters. Finally, we investigate the full distribution of the random variables that arise in the coverage depth problem, of which the traditionally studied expectation is just the first moment. This allows us to distinguish between code constructions that, at first glance, may appear to behave identically. |
| title | The Random Variables of the DNA Coverage Depth Problem |
| topic | Information Theory |
| url | https://arxiv.org/abs/2507.20645 |