Scaffolding and completing genome assemblies in real-time with nanopore sequencing

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Third-generation sequencing offers long reads for improved genome assemblies.
• Current methods are resource-intensive and analyze data post-sequencing, leading to inefficiencies.
• This results in either over-sequencing or low-quality assemblies due to under-sequencing.

Purpose of the Study:

• To introduce npScarf, a novel tool for real-time genome assembly scaffolding and completion.
• To enable dynamic termination of sequencing runs based on assembly quality metrics.

Main Methods:

• npScarf processes long-read sequencing data during the run.
• It scaffolds and completes existing short-read assemblies.
• Real-time assembly metrics guide sequencing run termination.

Main Results:

• npScarf successfully assembled bacterial and eukaryotic genomes.
• Achieved more complete and accurate assemblies than existing methods.
• Demonstrated reduced sequencing data and computational resource requirements.

Conclusions:

• npScarf provides a time- and resource-effective strategy for genome assembly.
• Enables efficient use of long-read sequencing data.
• Optimizes the genome assembly process by allowing real-time quality control.