Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.

ABSTRACT: Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing efforts, thus, cannot be re-focused on molecules likely contributing most to experimental success. Here we present BOSS-RUNS, an algorithmic framework and software to generate dynamically updated decision strategies. We quantify uncertainty at each genome position with real-time updates from data already observed. For each DNA fragment, we decide whether the expected decrease in uncertainty that it would provide warrants fully sequencing it, thus optimizing information gain. BOSS-RUNS mitigates coverage bias between and within members of a micr

SUBMITTER: Weilguny L 

PROVIDER: S-EPMC10344778 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature