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

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-11-04 DOI:10.1186/s13059-024-03423-3

Junhai Qi, Zhengyi Li, Yao-zhong Zhang, Guojun Li, Xin Gao, Renmin Han

引用次数: 0

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.

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TDFPS-Designer：纳米孔测序中条形码设计和选择的高效工具包

牛津纳米孔技术公司（ONT）提供超高通量多样品测序服务，但只提供最多可复用 96 个样品的条形码工具包。我们介绍的 TDFPS-Designer 是一种用于纳米孔测序条形码设计的新工具包，它能创建更多的条形码：137 个长度为 20 碱基对的条形码、410 个长度为 24 bp 的条形码和 1779 个长度为 30 bp 的条形码，远远超过了牛津纳米孔技术公司的产品。它包括基于 GPU 的加速功能，可实现超快的解复用，并设计出适用于高误差 ONT 数据的强大条形码。TDFPS-Designer 的性能优于当前的方法，与 Guppy 相比，它将解复用召回率提高了 20%，而精度却没有降低。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.