whole genome sequencing of Plasmodium falciparum using nanopore technology

Malaria parasite genomes have been generated predominantly using short read sequencing which can be slow, requires advanced training, and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform which 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. Nanopore has low error rates for haploid SNV genotyping and identifies structural variants (SVs) not detected with short reads. Nanopore genomes can be directly compared to publically available genomes and produce high quality end to end chromosome assemblies. Nanopore sequencing will expedite whole genome surveillance of malaria and provide new insights into parasite genome biology.