Document Type
Article
Journal Title
iScience
Publication Date
2024
Volume
27
Abstract
In this study, we assessed the quality of de novo genome assemblies for three species of parasitic nematodes (Brugia malayi, Trichuris trichiura, and Ancylostoma caninum) generated using only Oxford Nanopore Technologies MinION data. Assemblies were compared to current reference genomes and against additional assemblies that were supplemented with short-read Illumina data through polishing or hybrid assembly approaches. For each species, assemblies generated using only MinION data had similar or superior measures of contiguity, completeness, and gene content. In terms of gene composition, depending on the species, between 88.9 and 97.6% of complete coding sequences predicted in MinION data only assemblies were identical to those predicted in assemblies polished with Illumina data. Polishing MinION data only assemblies with Illumina data therefore improved gene-level accuracy to a degree. Furthermore, modified DNA extraction and library preparation protocols produced sufficient genomic DNA from B. malayi and T. trichiura to generate de novo assemblies from individual specimens.
DOI Link
ISSN
2589-0042
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Recommended Citation
Herzog, Kaylee; Wu, Rachel; Hawdon, John M.; Nejsum, Peter; and Fauver, Joseph R., "Assessing De Novo Parasite Genomes Assembled Using Only Oxford Nanopore Technologies MinION Data" (2024). Journal Articles: Epidemiology. 203.
https://digitalcommons.unmc.edu/coph_epidem_articles/203