Microsatellites, also known as short tandem repeats (STRs), are tracts of repetitive DNA sequences containing motifs ranging from two to six bases. Microsatellites are one of the most abundant type of variation in the human genome, after single nucleotide polymorphisms (SNPs) and Indels. Microsatellite analysis has a wide range of applications, including medical genetics, forensics and construction of genetic genealogy. However, microsatellite variations are rarely considered in whole-genome sequencing studies, in large due to a lack of tools capable of analyzing them.