Benchmarking of real-time, field-deployable whole-genome sequencing of Plasmodium falciparum using Nanopore technology.

Malaria parasite genomes have been generated predominantly using Illumina short-read sequencing that requires expensive equipment, is time-consuming with complex protocols, and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform generates long reads in real time and may overcome these limitations. We present compelling evidence that Nanopore sequencing delivers valuable additional information for malaria parasites with similar data fidelity for single nucleotide variant (SNV) calls compared to standard Illumina whole-genome sequencing. We demonstrate this through sequencing of pure Plasmodium falciparum DNA, mock infections and natural isolates from low-density, asymptomatic infections. Nanopore has low error rates for haploid SNV genotyping and identifies structural variants not detected with short reads. Nanopore genomes can be directly compared to publicly available genomes and produce high-quality end-to-end chromosome assemblies including complex, previously difficult-to-access regions. Nanopore sequencing could expedite whole-genome surveillance of malaria and provide new insights into parasite genome biology.