The expansion of short tandem repeats is a feature of over 60 different human diseases. Ongoing somatic expansion throughout a patient's lifetime can influence disease progression and may be harnessed for therapeutic interventions. Understanding its mechanism is essential for the rational identification of potential drug targets and small molecules. A major obstacle towards that translational goal has been to measure changes in repeat size in a timely manner. To address this, here we present Single Clone-based Instability Assay (SCIA), a streamlined experimental design that saves weeks in assessing the effect of a gene knockout on repeat instability. The approach avoids bulk cultures and does not require a reporter cell line. Instead, it uses long-read sequencing as a read out for repeat instability. We have validated the approach using FAN1, PMS1, and MLH1 knockouts in HEK293-derived cells. We opted to visualise the data with delta plots and extracted the instability frequency, the direction of the changes and their average size. This approach can be made PCR-free and used in a variety of cell lines, making it widely applicable. To facilitate use of the pipeline, we provide a software bundle for data visualization and statistical analysis.