Malaria infections are often “complex”, meaning they consist of several parasite strains co-circulating in the blood. Complex infections can arise due to multiple mosquito bites, and/or due to a single bite introducing several genotypes. Complex infections create a huge problem when it comes to genetic sequencing because the “phasing” of the genotypic data is lost. This means a genetic variation at a first locus may be known, and there is variation at a second locus, but its unclear which variation goes together.