title: WGS of 3D7 Plasmodium falciparum resistant to AN13762
design: Genomic DNA was extracted from parasite cultures (10 ml at 2% hematocrit and ~10% parasitemia) using the PureLink Genomic DNA Kit (Invitrogen) and extracted per manufacturers instructions. Paired-end next generation sequencing libraries were constructed from the gDNA using the NEBNext Ultra II kit (New England Biolabs). gDNA (200 ng) was enzymatically fragmented for 17.5 minutes at 37C, and the reaction was quenched with EDTA. The samples were cleaned with AMPure beads (Beckman Coulter) at a sample: bead ratio of 1:1.4 and eluted in sterile H2O. Eluted samples were run on a Bioanalyzer HS DNA kit (Agilent) to confirm the presence of 200-300 bp gDNA fragments. Samples were then subjected to end prep and adaptor ligation using a 1:10 dilution of the NEBNext Adaptor, all as described in the NEBNext Ultra II protocol. After digestion with the USER enzyme, a second AMPure bead clean-up was carried out with a sample:bead ratio of 1:0.9 for 15 min prior to placing the beads on a magnet and eluting with sterile H2O. Samples were then indexed with 9 cycles of PCR using NEB Q5 polymerase, unique TruSeq i5/i7 barcode primers, and conditions according to the NEB Q5 protocol. A final AMPure bead clean-up step was performed at a sample:bead ratio of 1:0.9, with elution with sterile H2O. Library quality was assessed with a Bioanalyzer HS DNA kit, with broad peaks from 200 to 500 bp observed in each sample, as expected. Libraries were pooled and sequenced on an Illumina Hi-Seq 4000 using a PE100 flow cell.  Paired reads were combined and analyzed as single reads.