Easy reference-guided assembly of nanopore whole plasmid sequencing datasets

IF 2.5 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry Pub Date : 2025-09-05 DOI:10.1016/j.ab.2025.115970

Vinita Sharma , Naiyu Jiang , Yukihiro Nagashima , Hisashi Koiwa

引用次数: 0

Abstract

Whole plasmid sequencing (WPS) using Nanopore long read sequencing has emerged as a cost-effective alternative for dideoxy sequencing methods. De novo sequence assembly for large plasmids, however, are not always successful and may produce large assembly gaps. Here we streamlined a reference-guided alignment of WPS nanopore reads using galaxy platform. The process is straightforward and facilitate introduction of WPS as an alternative for researchers who are more used to dideoxy sequencing platform. We demonstrate that our procedure can assemble nanopore sequence reads with different quality datasets and identify variations from reference sequence.

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易于参考引导组装纳米孔全质粒测序数据集。

利用纳米孔长读测序的全质粒测序（WPS）已成为二脱氧测序方法的一种具有成本效益的替代方法。然而，大型质粒的从头序列组装并不总是成功的，并且可能产生较大的组装间隙。本研究利用星系平台简化了WPS纳米孔reads的参考导向比对。该过程简单明了，便于引入WPS作为更习惯于二脱氧测序平台的研究人员的替代方案。我们证明了我们的程序可以用不同质量的数据集组装纳米孔序列，并识别参考序列的差异。

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

Analytical biochemistry 生物-分析化学

CiteScore

5.70

自引率

0.00%

发文量

283

审稿时长

44 days

期刊介绍： The journal''s title Analytical Biochemistry: Methods in the Biological Sciences declares its broad scope: methods for the basic biological sciences that include biochemistry, molecular genetics, cell biology, proteomics, immunology, bioinformatics and wherever the frontiers of research take the field. The emphasis is on methods from the strictly analytical to the more preparative that would include novel approaches to protein purification as well as improvements in cell and organ culture. The actual techniques are equally inclusive ranging from aptamers to zymology. The journal has been particularly active in: -Analytical techniques for biological molecules- Aptamer selection and utilization- Biosensors- Chromatography- Cloning, sequencing and mutagenesis- Electrochemical methods- Electrophoresis- Enzyme characterization methods- Immunological approaches- Mass spectrometry of proteins and nucleic acids- Metabolomics- Nano level techniques- Optical spectroscopy in all its forms. The journal is reluctant to include most drug and strictly clinical studies as there are more suitable publication platforms for these types of papers.