Genome assembly using Nanopore-guided long and error-free DNA reads

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Long-read sequencing technologies promise to overcome challenges in assembling large and complex genomes.
• Existing long-read technologies have limitations for many research labs and large-scale projects.
• Oxford Nanopore's MinION® device offers a low-cost, single-molecule nanopore sequencing option for long DNA fragments.

Purpose of the Study:

• To develop a hybrid approach for assembling genomes using long reads from the Oxford Nanopore MinION® device.
• To address the challenge of high error rates in MinION® reads for genome assembly.
• To generate highly contiguous and accurate genome assemblies, particularly for microbial genomes.

Main Methods:

• A hybrid sequencing strategy combining Oxford Nanopore MinION® and Illumina data.
• Development of a method to generate Nanopore Synthetic-long (NaS) reads up to 60 kb.
• Application of the hybrid approach to sequence the bacterium Acinetobacter baylyi ADP1.

Main Results:

• Achieved a highly contiguous genome assembly of Acinetobacter baylyi ADP1 in a single contig.
• Generated NaS reads with 99.99% average accuracy, spanning repetitive regions without errors.
• Demonstrated superior assembly contiguity and accuracy compared to an Illumina-only assembly.

Conclusions:

• The NaS tool provides an efficient and cost-effective hybrid approach for microbial genome sequencing using MinION®.
• The method is suitable for small facilities and enables rapid genome sequencing.
• Oxford Nanopore technology, despite its current error rate, is valuable for generating high-quality genome assemblies.