Fig. 1: Design of long-range multiplex PCRs for the low-complexity P. falciparum genome using multiply. | Nature Communications

Fig. 1: Design of long-range multiplex PCRs for the low-complexity P. falciparum genome using multiply.

From: Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing

Fig. 1

a Multiplex PCR primer design workflow by multiply. An optimal set of primers is selected from a large candidate pool; minimising SNPs in primer binding sites, primer dimers, and off-target primer binding with a cost function. b Schematic of a cost-effective protocol for targeted nanopore sequencing of P. falciparum malaria from dried blood spots (DBS) that takes three days and costs ~ USD $25 per sample. c Histograms of crt and (d) kelch13 coverage stratified by read length. (A+T) percentage in 20bp sliding widows (blue) and homopolymer run length (red) are shown, as well as a heatmap of nucleotide composition. For both genes the entire coding sequence (CDS) is covered in the majority of reads. e Read length distributions for NOMADS8 (left, 28.8 kbp total) and NOMADS16 (right, 54.7 kbp total) amplicon panels. Grey triangle indicates coding sequence (CDS) length. Amplicons were designed to be 3–4 kbp. Marginal distribution for all amplicons displayed at top. Data for (c–e) are from a mock sample created from P. falciparum 3D7 and human DNA (Methods).

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