Sequencing Coverage Analysis for Combinatorial DNA-Based Storage Systems

• Published in: IEEE transactions on molecular, biological, and multi-scale communications Vol. 10; no. 2; pp. 297 - 316
• Main Authors: Preuss, Inbal, Galili, Ben, Yakhini, Zohar, Anavy, Leon
• Format: Journal Article
• Language: English
• Published: Piscataway IEEE 01.06.2024; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Combinatorial analysis; Computational biology; Confidence intervals; Data storage; Decoding; Design parameters; DNA; DNA data storage; DNA-based data storage; Encoding; Error correction; Gene sequencing; Markov chains; Memory; Messages; Reconstruction; Statistical analysis; Storage systems; synthethic biology; Synthetic biology; Tightness
• ISSN: 2372-2061; 2372-2061
• DOI: 10.1109/TMBMC.2024.3408053

This study introduces a novel model for analyzing and determining the required sequencing coverage in DNA-based data storage, focusing on combinatorial DNA encoding. We seek to characterize the distribution of the number of sequencing reads required for message reconstruction. We use a variant of the coupon collector distribution for this purpose. For any given number of observed reads, <inline-formula> <tex-math notation="LaTeX">R\in \mathbb {N} </tex-math></inline-formula>, we use a Markov Chain representation of the process to compute the probability of error-free reconstruction. We develop theoretical bounds on the decoding probability and use empirical simulations to validate these bounds and assess tightness. This work contributes to understanding sequencing coverage in DNA-based data storage, offering insights into decoding complexity, error correction, and sequence reconstruction. We provide a Python package, with its input being the code design and other message parameters, all of which are denoted as <inline-formula> <tex-math notation="LaTeX">\boldsymbol {\Theta } </tex-math></inline-formula>, and a desired confidence level <inline-formula> <tex-math notation="LaTeX">1-\delta </tex-math></inline-formula>. This package computes the required read coverage, guaranteeing the message reconstruction <inline-formula> <tex-math notation="LaTeX">R=R(\delta,\boldsymbol {\Theta }) </tex-math></inline-formula>.