Sequence capture of WW2: H6
We extracted DNA from avian blood using a standard ethanol based extraction protocol. We tested for haemosporidian DNA with nested PCR and sequenced haemosporidian cytochrome b with Sanger sequencing to confirm haemosporidian species and lineage. We captured targeted regions of the extracted DNA using a myBaits Hybridization Capture for Targeted NGS Kit with the Swift Biosciences Accel-NGS 2S Hyb DNA Library Kit and KAPA HiFi HotStart ReadyMix PCR Kit. To do this, we sheared the 48 DNA samples using an M220 Focused-ultrasonicator (Covaris, MA, USA) and then built indexed Illumina libraries from all samples. We next made six pools, each made up of eight libraries at equimolar concentrations, and we performed the sequence capture on each pool separately. We sequenced the captured DNA on an Illumina MiSeq.