Easy reference-guided assembly of nanopore whole plasmid sequencing datasets

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Whole plasmid sequencing (WPS) using Nanopore long-read technology is a cost-effective alternative to traditional dideoxy sequencing.
• De novo assembly of large plasmids can be challenging, often resulting in assembly gaps.
• Researchers accustomed to dideoxy sequencing may find Nanopore-based methods less accessible.

Purpose of the Study:

• To streamline the reference-guided alignment of Nanopore WPS reads.
• To simplify the introduction of WPS for researchers familiar with dideoxy sequencing.
• To demonstrate a robust method for assembling Nanopore sequence reads and identifying variations.

Main Methods:

• Developed a reference-guided alignment workflow for Nanopore WPS reads.
• Utilized the Galaxy platform for streamlined data analysis.
• Tested the procedure with Nanopore sequence reads from varying quality datasets.

Main Results:

• Successfully assembled Nanopore sequence reads using the streamlined workflow.
• Demonstrated the method's effectiveness across different quality datasets.
• Accurately identified variations from reference sequences.

Conclusions:

• The streamlined reference-guided alignment process facilitates the adoption of Nanopore WPS.
• This method provides a viable and cost-effective alternative to dideoxy sequencing for plasmid analysis.
• The procedure reliably assembles Nanopore reads and detects sequence variations.