Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.
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DOI：
10.1038/s41587-022-01580-z
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发表时间：
2023-07
影响因子：
46.9
通讯作者：
Goldman, Nick
中科院分区：
文献类型：
--
作者：
Weilguny, Lukas;De Maio, Nicola;Munro, Rory;Manser, Charlotte;Birney, Ewan;Loose, Matthew;Goldman, Nick
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 microbial community, leading to improved variant calling; for example, low-coverage sites of a species at 1% abundance were reduced by 87.5%, with 12.5% more single-nucleotide polymorphisms detected. Such data-driven updates to molecule selection are applicable to many sequencing scenarios, such as enriching for regions with increased divergence or low coverage, reducing time-to-answer. Nanopore selective sequencing with real-time decision updates mitigates coverage bias.
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DOI：
10.1093/noajnl/vdab149
发表时间：
2021-01
期刊：
Neuro-oncology advances
影响因子：
--
作者：
Djirackor L;Halldorsson S;Niehusmann P;Leske H;Capper D;Kuschel LP;Pahnke J;Due-Tønnessen BJ;Langmoen IA;Sandberg CJ;Euskirchen P;Vik-Mo EO
通讯作者：
Vik-Mo EO
影响因子：
4.6
作者：
Barbitoff, Yury A.;Polev, Dmitrii E.;Predeus, Alexander V.
通讯作者：
Predeus, Alexander V.
使用Oxford Nanopore的自适应测序评估人类阴道样品中微生物组富集和宿主DNA耗竭的评估。
影响因子：
4.6
作者：
Marquet M;Zöllkau J;Pastuschek J;Viehweger A;Schleußner E;Makarewicz O;Pletz MW;Ehricht R;Brandt C
通讯作者：
Brandt C
影响因子：
12.3
作者：
Martin S;Heavens D;Lan Y;Horsfield S;Clark MD;Leggett RM
通讯作者：
Leggett RM
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng