Low-depth Raw Reads of Nanopore Sequencing Enables Rapid and Accurate Bacterial Identification

The recent advent of third-generation sequencing technologies brings promise for better bacterial identification. However, the commercial applications of the current sequencing technologies are still constrained since their high cost and error rate of this sequencing technology. Thus, strategies for time-saving bacterial identification with low cost and high accuracy are urgently needed. In this study, we evaluated the performance of the Nanopore long-read sequencer and the Illumina platform alone or in combination with different data volume (0.5–80×) after assembly, to ascertain whether the incomplete genomes enable accurate bacterial identification. The results showed that the average nucleotide identity value of hybrid assembly and Illumina assembly does not change much as the amount of data increases. In addition, the ANI value reached a plateau at 5×, while the ANI values of Nanopore-only assemblies increased in the range of 5–30×. Since the assembly process was time-consuming, this study compared the accuracy of the Nanopore long-read sequencer in species identification with various sets of the reads (0.5–80×), to further confirm the minimum amount of data required for accurate bacteria identification. Without assembly, it enabled rapid and accurate bacterial identification with low coverage of Nanopore raw reads (0.5×). The results of study suggested the potential of Nanopore sequencing in rapid bacteria identification using low-depth raw reads (0.5×) without assembly, and provided data basis in developing new strategy for bacterial identification.