Abstract
SUMMARY: TRACK is a user-friendly Snakemake workflow designed to streamline the discovery and comparison of tandem repeats (TRs) across species. TRACK facilitates the cataloging and filtering of TRs based on reference genomes or T2T transcripts, and applies reciprocal LiftOver and sequence alignment methods to identify putative homologous TRs between species. For further analyses, TRACK can be used to genotype TRs and subsequently estimate and plot basic population genetic statistics. By incorporating key functionalities within an integrated workflow, TRACK enhances TR analysis accessibility and reproducibility, while offering flexibility for the user. AVAILABILITY AND IMPLEMENTATION: The TRACK toolkit with step-by-step tutorial is freely available at https://github.com/caroladam/track.