High quality MinION and Flongle long-read nanopore genome assemblies of Mycoplasma bovis using taxon-specific training of the Bonito basecaller

Implementation of Third-Generation Sequencing for WGS all-in-one diagnostics in human and veterinary medicine requires rapid and accurate generation of consensus genomes. Nevertheless, obtaining high quality genomes from non-standard organisms is still not guaranteed. This is the case for Mycoplasma bovis, an important respiratory pathogen in cattle. Current complete diagnostics require molecular and time-consuming culture-based approaches. Implementation of cheap and quick long read all-in-one WGS approaches are only feasible if increased genome accuracies and completeness can be obtained. Here, a taxon-specific custom-trained Bonito v.0.1.3 model (custom-pg45) was implemented in various WGS assembly bioinformatics pipelines. We showed improved completeness and overall consensus accuracies up to Q45.2 and Q46.7 for reference-based and Canu de novo assembled M. bovis genomes, respectively. Furthermore, the custom-pg45 model was applicable for another ten M. bovis field strains. These results implicate that taxon-specific basecalling of MinION and single-use Flongle Nanopore long reads are of great value to be implemented in rapid all-in-one WGS tools as evidenced for Mycoplasma bovis as an example.