Abstract
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol interference, and noisy measurements by concatenating an i.i.d. duplication channel with a finite-state semi-Markov channel. Compared to previous models, this channel models the dominant distortions of the nanopore while remaining tractable. Anticipating future coding schemes, we derive MAP detection algorithms and estimate achievable rates. Given that finite-state semi-Markov channels are a subclass of channels with memory, we conjecture that the achievable rate of the noisy nanopore channel can be optimised using a variation of the generalised Blahut-Arimoto algorithm.
| Original language | English |
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| Title of host publication | 2022 IEEE International Symposium on Information Theory, ISIT 2022 |
| Editors | Muriel Médard, Mikael Skoglund, Aylin Yener |
| Place of Publication | Piscataway NJ USA |
| Publisher | IEEE, Institute of Electrical and Electronics Engineers |
| Pages | 216-221 |
| Number of pages | 6 |
| ISBN (Electronic) | 9781665421591 |
| ISBN (Print) | 9781665421607 |
| DOIs | |
| Publication status | Published - 2022 |
| Event | IEEE International Symposium on Information Theory 2022 - Espoo, Finland Duration: 26 Jun 2022 → 1 Jul 2022 https://ieeexplore.ieee.org/xpl/conhome/9834325/proceeding (Proceedings) https://www.isit2022.org/ (Website) |
Publication series
| Name | IEEE International Symposium on Information Theory - Proceedings |
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| Publisher | IEEE, Institute of Electrical and Electronics Engineers |
| Volume | 2022-June |
| ISSN (Print) | 2157-8095 |
| ISSN (Electronic) | 2157-8117 |
Conference
| Conference | IEEE International Symposium on Information Theory 2022 |
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| Abbreviated title | ISIT 2022 |
| Country/Territory | Finland |
| City | Espoo |
| Period | 26/06/22 → 1/07/22 |
| Internet address |
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