Simulated ONT libraries for genome assembly experimental design

Background: High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences in excess of 100,000 nucleotides but high error rates make sequence assembly and analysis a non-trivial problem as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly but few studies have attempted to address eukaryotic organisms. Here, we present novel results using a combination of simulated and empirical ONT and DNA libraries and identify best practices for ONT sequencing and assembly. We simulate ONT and Illumina DNA sequence reads for Escherichia coli, Caenorhabditis elegans, Arabidopsis thaliana, and Drosophila melanogaster and assemble with Canu, Flye, and MaSuRCA software to quantify the influence of sequencing coverage and assembly approach. We show broad applicability of our methods using real ONT data generated for four strains of the nematode Caenorhabditis r...