TRACKing Tandem Repeats: a customizable pipeline for identification and cross-species comparisons

Abstract

SummaryTRACK is a user-friendly command-line pipeline designed to consolidate 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 streamlined analyses, TRACK can be used to genotype TRs and subsequently estimate and plot basic population genetic statistics. By integrating existing tools into one integrated workflow, TRACK enhances TR analysis accessibility and reproducibility, while offering flexibility for the user. AvailabilityThe TRACK toolkit with step-by-step tutorial is freely available at https://github.com/caroladam/track.