BioProject

Implementation of Third-Generation Sequencing for Whole Genome Sequencing (WGS) all-in-one diagnostics in human and veterinary medicine requires rapid and accurate generation of consensus genomes. Nevertheless, obtaining high quality genomes from not-frequently sequenced organisms is still not guaranteed. This is the case for Mycoplasma bovis, an important respiratory pathogen in cattle. Mycoplasma spp. exhibit distinct genomic characteristics within the small (<1 Mbp) genomes, including low GC content, highly repetitive regions, and distinct methylation patterns. These features are commonly known to potentially result in sequencing bias when using short-read Illumina sequencing. Since current complete diagnostics require molecular and time-consuming culture-based approaches, implementation of cheap and quick long read all-in-one WGS approaches are of interest. This is only feasible if a high genome accuracy and completeness can be obtained. Here, a taxon-specific custom-trained Bonito v.0.1.3 basecalling model (custom-pg45) was implemented in various WGS assembly bioinformatics pipelines. This resulted in significantly lower errors within the genome assemblies of M. bovis field strain genomes, as compared to the default Guppy basecaller. Similar improvements were obtained when applied to sequencing output from the single-use Flongle, implicating both MinION and Flongle nanopore long-read sequencing can be confidently implemented in rapid all-in-one WGS diagnostics.