In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. A set of high-quality STR loci (6,768 from P. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. They are an important source of genetic diversity and can also have functional impact.
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