title: Illumina HiSeq of P. falciparum: adult tooth
design: DNA extracts were converted into double-stranded libraries suitable for sequencing on the Illumina platform with modifications from existing protocols (Meyer and Kircher, 2010; Kircher, Sawyer, and Meyer, 2012). Libraries for each extract were prepared in two ways: blunt end repair with Uracil-DNA Glycosylase (UDG) and Endonuclease VIII (EndoVIII) treatment to remove deaminated cytosine residues; and, blunt end repair without removal of cytosine residues (non-UDG/EndoVIII). MinElute PCR Purification (Qiagen) was applied between library preparation steps (blunt-end repair, adapter ligation, and adapter fill-in). Heat deactivation (80°C for 20 minutes) was performed after the fill-in stage.