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.