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