USAT: a Bioinformatic Toolkit to Facilitate Interpretation and Comparative Visualization of Tandem Repeat Sequences

Tandem repeats (TR), which are highly variable genomic variants, are widely used in individual identification, disease diagnostics and evolutionary studies. The recent advances of sequencing technologies and bioinformatic tools facilitate calling TR haplotypes. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision to characterize TR haplotypes. Analysis of the differences between or among TR haplotypes, especially at the single nucleotide level, is the focus of TR haplotype characterization. In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which includes allele size conversion, sequence comparison of haplotypes, figure plotting and comparison for allele distribution, and interactive visualization. An example application of USAT for analysis of the CODIS core STR loci with benchmarking human individuals demonstrated the capabilities of USAT. USAT has a user-friendly graphic interface and runs in all major computing operating systems at a fast speed with parallel computing enabled. In summary, USAT is able to facilitate the interpretation, visualization, and comparisons of TRs.