Short tandem repeats (STRs), also known as microsatellites, have a wide range of applications, including medical genetics, forensics, and population genetics. High-throughput sequencing has the potential to profile large numbers of STRs, but cumbersome gapped alignment and STR-specific noise patterns hamper this task. We recently developed an algorithm, called lobSTR, to overcome these challenges and to accurately profile STRs from short reads. Here we describe how to use lobSTR to call STR variations from high-throughput sequencing datasets and to diagnose the quality of the calls.