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(a) Bioinformatic pipeline for analysis of individual reads acquired from multiplex sequencing on an Ion Torrent 318 chip. (b) Number of reads assigned to each barcode in control DNA mixtures. (c) Number of reads assigned to each barcode in field-collected parasites. Coverage map across amplicon for pf-csp (d), pf-ama1 (e), and pf-k13 (f,g). False discovery rates at varying minor allele frequencies for reads from each gene target.
