Sequencing by Emergence: Modeling and Estimation

Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE promises to deliver accurate, ultra-long, haplotype-phased reads...

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Bibliographic Details
Published inarXiv.org
Main Authors Boyd, Nicholas, Woodhouse, Samuel, Kalim Mir
Format Paper Journal Article
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 03.08.2021
Subjects
Algorithms
Deoxyribonucleic acid
DNA
Gene sequencing
Nucleic acids
Probabilistic models
Quantitative Biology - Genomics
Statistics - Applications
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Summary:Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE promises to deliver accurate, ultra-long, haplotype-phased reads at the whole genome-scale for very low cost within 10 minutes. The data SEQE generates requires entirely new inference techniques. In this paper we introduce a probabilistic model of the SEQE measurement process and an algorithm that estimates sequence by solving a convex relaxation of the corresponding maximum likelihood problem. We demonstrate the effectiveness of our algorithm on a variety of simulated datasets.
ISSN:2331-8422
DOI:10.48550/arxiv.2103.10477