Work

TRACKing tandem repeats: a customizable pipeline for identification and cross-species comparison

Year: 2024

Type: article

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.

Source: Bioinformatics Advances

DOI: 10.1093/bioadv/vbaf066

Authors: Carolina L Adam, Joana Rocha, Peter Sudmant, Rori Rohlfs

Institutions: University of Oregon, University of California, Berkeley

Language: English

Topic: Chromosomal and Genetic Variations

Subfield: Plant Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,917

Funder: National Science Foundation