Assessment of Nanopore adaptive sampling for Plasmodium whole-genome sequencing

The predominance of human DNA in a malaria patient blood sample requires time-consuming lab procedures to filter out human DNA or enrich Plasmodium DNA. Here, we investigated the potential of adaptive sampling to enrich for Plasmodium DNA while sequencing unenriched patient blood samples on a minION device. In the first experiment (ERS14258240), we compared adaptive sampling to regular sequencing on a dilution series of human DNA (Promega G304A) mixed with Plasmodium falciparum 3D7 DNA. In the second experiment, we sequenced two patient samples using the adaptive sampling feature and assessed the quality of the obtained data in light of clinical applications. For these samples, reads mapping to the Plasmodium falciparum reference genome were made available under sample accessions ERS14258238 and ERS14258239.