Assessing Parasite Genomes Assembled Using Only Oxford Nanopore Technologies MinION Data

Overview

Journal iScience

Publisher Cell Press

Date 2024 Aug 30

PMID 39211578

Authors

Kaylee S Herzog

Rachel Wu

John M Hawdon

Peter Nejsum

Joseph R Fauver

Affiliations

Soon will be listed here.

Abstract

In this study, we assessed the quality of genome assemblies for three species of parasitic nematodes (, , and ) 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 and to generate assemblies from individual specimens.

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