• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

TDFPS-Designer：一种用于纳米孔测序中条码设计和选择的高效工具包。

TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.

机构信息

Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, China.

Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.

出版信息

Genome Biol. 2024 Nov 4;25(1):285. doi: 10.1186/s13059-024-03423-3.

DOI:10.1186/s13059-024-03423-3
PMID:39497190
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11533379/
Abstract

Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore sequencing barcode design, which creates significantly more barcodes: 137 with a length of 20 base pairs, 410 at 24 bp, and 1779 at 30 bp, far surpassing ONT's offerings. It includes GPU-based acceleration for ultra-fast demultiplexing and designs robust barcodes suitable for high-error ONT data. TDFPS-Designer outperforms current methods, improving the demultiplexing recall rate by 20% relative to Guppy, without a reduction in precision.

摘要

牛津纳米孔技术（ONT）提供超高通量多样本测序，但仅提供最多可实现 96 个样本多重化的条码试剂盒。我们介绍 TDFPS-Designer，这是一个用于纳米孔测序条码设计的新工具包，它可创建数量显著更多的条码：20 个碱基对长度的条码有 137 个，24 个碱基对长度的条码有 410 个，30 个碱基对长度的条码有 1779 个，远远超过 ONT 的产品。它包括基于 GPU 的加速超快速分拆，以及设计适合高错误率 ONT 数据的鲁棒条码。与 Guppy 相比，TDFPS-Designer 提高了分拆召回率 20%，而精度没有降低。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/45a1ca7dce26/13059_2024_3423_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/ce5313e22702/13059_2024_3423_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/46fcf19833a4/13059_2024_3423_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/f5c32d70e04e/13059_2024_3423_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/a26437c8bbac/13059_2024_3423_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/80a6b0781d90/13059_2024_3423_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/41d3ea4e2d3f/13059_2024_3423_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/626a1454bea8/13059_2024_3423_Figa_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/45a1ca7dce26/13059_2024_3423_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/ce5313e22702/13059_2024_3423_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/46fcf19833a4/13059_2024_3423_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/f5c32d70e04e/13059_2024_3423_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/a26437c8bbac/13059_2024_3423_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/80a6b0781d90/13059_2024_3423_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/41d3ea4e2d3f/13059_2024_3423_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/626a1454bea8/13059_2024_3423_Figa_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c43/11533379/45a1ca7dce26/13059_2024_3423_Fig7_HTML.jpg

相似文献

1
TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.TDFPS-Designer：一种用于纳米孔测序中条码设计和选择的高效工具包。
Genome Biol. 2024 Nov 4;25(1):285. doi: 10.1186/s13059-024-03423-3.
2
ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4.ONTbarcoder 2.0：通过牛津纳米孔 R10.4 实现实时条形码辅助的快速物种发现和鉴定。
Cladistics. 2024 Apr;40(2):192-203. doi: 10.1111/cla.12566. Epub 2023 Dec 2.
3
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing.HycDemux：一种用于纳米孔测序中准确进行带条码样本解复用的混合无监督方法。
Genome Biol. 2023 Oct 5;24(1):222. doi: 10.1186/s13059-023-03053-1.
4
Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing.可扩展、具有成本效益且去中心化的 DNA 条形码技术，结合牛津纳米孔测序。
Methods Mol Biol. 2024;2744:223-238. doi: 10.1007/978-1-0716-3581-0_14.
5
Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.体内排列条形码用于质粒 DNA 的多重序列验证和混合库的解复用。
Nucleic Acids Res. 2024 Jun 10;52(10):e47. doi: 10.1093/nar/gkae332.
6
Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free.准备就绪：纳米孔代谢组条形码现在可以恢复高度准确的共识条形码，通常无插入/缺失。
BMC Genomics. 2024 Sep 9;25(1):842. doi: 10.1186/s12864-024-10767-4.
7
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data.基准测试显示深度学习变异调用程序在细菌纳米孔测序数据上的优越性。
Elife. 2024 Oct 10;13:RP98300. doi: 10.7554/eLife.98300.
8
Complete pipeline for Oxford Nanopore Technology amplicon sequencing (ONT-AmpSeq): from pre-processing to creating an operational taxonomic unit table.牛津纳米孔技术扩增子测序（ONT-AmpSeq）的完整流程：从预处理到创建操作分类单元表。
FEBS Open Bio. 2024 Nov;14(11):1779-1787. doi: 10.1002/2211-5463.13868. Epub 2024 Aug 7.
9
Takeaways from Mobile DNA Barcoding with BentoLab and MinION.从 BentoLab 和 MinION 的移动 DNA 条形码中获得的经验。
Genes (Basel). 2020 Sep 24;11(10):1121. doi: 10.3390/genes11101121.
10
Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota.Illumina 与 Nanopore 16S rRNA 基因测序技术在人类鼻腔微生物组中的比较。
Genes (Basel). 2020 Sep 21;11(9):1105. doi: 10.3390/genes11091105.

本文引用的文献

1
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing.纳米孔直接 RNA 测序的测序准确性和系统误差。
BMC Genomics. 2024 May 28;25(1):528. doi: 10.1186/s12864-024-10440-w.
2
Simulation of nanopore sequencing signal data with tunable parameters.可调参数的纳米孔测序信号数据模拟。
Genome Res. 2024 Jun 25;34(5):778-783. doi: 10.1101/gr.278730.123.
3
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing.HycDemux：一种用于纳米孔测序中准确进行带条码样本解复用的混合无监督方法。
Genome Biol. 2023 Oct 5;24(1):222. doi: 10.1186/s13059-023-03053-1.
4
Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning.通过无监督机器学习对纳米孔测序原始信号进行条形码解复用。
Front Bioinform. 2023 Apr 27;3:1067113. doi: 10.3389/fbinf.2023.1067113. eCollection 2023.
5
Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing.利用纳米孔测序鉴定 SARS-CoV-2 的基因组变异。
Medicina (Kaunas). 2022 Dec 15;58(12):1841. doi: 10.3390/medicina58121841.
6
Active learning for efficient analysis of high-throughput nanopore data.基于主动学习的高通量纳米孔数据分析方法。
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac764.
7
De novo assembly of human genome at single-cell levels.单细胞水平的人类基因组从头组装。
Nucleic Acids Res. 2022 Jul 22;50(13):7479-7492. doi: 10.1093/nar/gkac586.
8
RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.RATTLE：基于纳米孔测序的无参转录组重构和定量分析。
Genome Biol. 2022 Jul 8;23(1):153. doi: 10.1186/s13059-022-02715-w.
9
Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer.使用 MinION 纳米孔测序仪进行多重扩增子测序以识别突变的概念验证。
Sci Rep. 2022 May 20;12(1):8572. doi: 10.1038/s41598-022-12613-7.
10
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing.利用超快纳米孔基因组测序加速致病变异体的鉴定。
Nat Biotechnol. 2022 Jul;40(7):1035-1041. doi: 10.1038/s41587-022-01221-5. Epub 2022 Mar 28.