Assessing the quality of de novo parasite genomes assembled using only Oxford Nanopore Technologies MinION data
Streamlined laboratory and computational workflows to generate high-quality reference genomes from individual specimens using a single data source have the potential to increase the availability of genomic data from parasitic nematodes. In this study, we aimed to compare the contiguity, completeness, and gene content from de novo genome assemblies generated only with data from the Oxford Nanopore Technologies (ONT) MinION sequencing platform to assemblies supplemented with Illumina sequencing data. Three species of parasitic nematodes (Brugia malayi, Trichuris trichuria, and Ancylostoma caninum) were included in our study. We generated and compared three de novo assembly approaches for each species: MinION data only, MinION data only polished with Illumina data, and a hybrid assembly that uses both MinION and Illumina data as input. Each approach produced assemblies with comparable quality metrics for each of the three species assessed. This study demonstrates that ONT MinION data generated from individual nematodes is sufficient to construct highly contiguous and complete de novo whole genome assemblies, highlighting an accessible method for helminth genome generation.