PRJNA505368
Evaluation of De novo assembly of bacterial genomes with rapid MinION sequencing platform
Complete genome sequences of organisms are the foundation of understanding biological functions. High-throughput parallel sequencing technologies such as Illumina make the bacterial genomic analyses possible and efficient, and benefit public health and basic bacterial related research. The short-read platforms have limits of resolving complete genome sequences and complex genomic structures. Long-read data generated by Oxford Nanopore Technologies (ONT) show great potential in finishing complete bacterial genomes. In this study, we evaluated the ability of ONT in completing bacterial genomes for twelve different species of both gram-negative and gram-positive bacteria. Bacterial genomes can be completed when the data volume is larger than 20×coverage of the genome in average, although manual curations are needed in certain circumstances. Importantly, de novo assembly of genomes based on ONT reads could be affected by assembly tools, some of which may result in misassembled genomes. Careful comparison of assembly results of various tools should be conducted before obtaining accurate results. With the improvement of ONT read quality and platforms, the discrepancy of assemblies between assembly tools may disappear in future. Also, finishing multiple genomes (twelve or more) of different bacterial species in a single MinION run with a rapid library preparation method are becoming possible as the technology improves.