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使用readfish大规模增强PromethION的纳米孔自适应采样。

Enhancing nanopore adaptive sampling for PromethION using readfish at scale.

作者信息

Munro Rory, Payne Alexander, Holmes Nadine, Moore Chris, Cahyani Inswasti, Loose Matthew

机构信息

School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.

Deepseq, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.

出版信息

Genome Res. 2025 Apr 14;35(4):877-885. doi: 10.1101/gr.279329.124.

DOI:10.1101/gr.279329.124
PMID:39884748
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12047233/
Abstract

A unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling all features for the industrial scale PromethION sequencer, including standard and "barcode-aware" adaptive sampling. We demonstrate effective coverage enrichment and assessment of multiple human genomes for copy number and structural variation on a single PromethION flow cell.

摘要

牛津纳米孔技术测序仪的一个独特功能——自适应采样，可从测序文库中精确选择DNA分子。在此，我们展示了对我们的工具readfish的改进，使其具备适用于工业规模PromethION测序仪的所有功能，包括标准和“条形码感知”自适应采样。我们在单个PromethION流动槽上展示了对多个人类基因组进行有效覆盖富集以及对拷贝数和结构变异的评估。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/4de5ef40ce88/877f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/86e7c4542a78/877f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/31cb5c5d625a/877f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/fa0da62ccf47/877f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/55a648a5ee10/877f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/4de5ef40ce88/877f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/86e7c4542a78/877f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/31cb5c5d625a/877f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/fa0da62ccf47/877f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/55a648a5ee10/877f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f045/12047233/4de5ef40ce88/877f05.jpg

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Non-invasive real-time genomic monitoring of the critically endangered kākāpō.对极度濒危的鸮鹦鹉进行非侵入性实时基因组监测。
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A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing.一种用于病毒扩增子纳米孔测序的实时监测、分析和自适应采样的框架。
Front Genet. 2023 Mar 27;14:1138582. doi: 10.3389/fgene.2023.1138582. eCollection 2023.
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Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.利用贝叶斯实验设计在纳米孔测序中进行动态自适应采样。
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