Computational tools for tandem repeat detection using long-read sequencing.

Abstract

Tandem repeats (TRs) play essential roles in a variety of biological functions, and their abnormal expansions are significantly implicated in phenotypic variation and cause >60 human diseases. However, long TR regions cannot be reliably detected using short-read sequencing, and long-read sequencing enables accurate genome-wide detection of TRs. In recent years, various computational tools have been developed to detect and genotype TRs from long-read data. In this survey, we systematically categorize and review 39 computational tools designed for TR detection, visualization and functional interpretation. We discuss their strengths and limitations for TR detection from long-read sequencing data, highlighting current challenges and future directions to advance long-read TR detection methodologies.