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Technical Program

Paper Detail

Paper IDD5-S7-T4.3
Paper Title On Coding for an Abstracted Nanopore Channel for DNA Storage
Authors Reyna Hulett, Shubham Chandak, Mary Wootters, Stanford University, United States
Session D5-S7-T4: Trace Reconstruction & Coding for DNA Storage
Chaired Session: Saturday, 17 July, 00:00 - 00:20
Engagement Session: Saturday, 17 July, 00:20 - 00:40
Abstract 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, it is cheap, portable, and can support longer reads. While several practical coding schemes have been developed for DNA storage with nanopore sequencing, the theory is not well understood. Towards that end, we study a highly abstracted (deterministic) version of the nanopore sequencer, which highlights key features that make its analysis difficult. We develop methods and theory to understand the capacity of our abstracted model, and we propose efficient coding schemes and algorithms.