追踪串联重复序列：用于识别和跨物种比较的可定制流程
TRACKing tandem repeats: a customizable pipeline for identification and cross-species comparison.
作者信息
Adam Carolina L, Rocha Joana, Sudmant Peter, Rohlfs Rori
机构信息
Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, United States.
Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, United States.
出版信息
Bioinform Adv. 2025 Apr 8;5(1):vbaf066. doi: 10.1093/bioadv/vbaf066. eCollection 2025.
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.
摘要
TRACK是一个用户友好的Snakemake工作流程，旨在简化跨物种串联重复序列（TR）的发现和比较。TRACK有助于基于参考基因组或T2T转录本对TR进行编目和筛选，并应用相互的LiftOver和序列比对方法来识别物种间假定的同源TR。为了进行进一步分析，TRACK可用于对TR进行基因分型，随后估计并绘制基本的群体遗传统计数据。通过在一个集成的工作流程中纳入关键功能，TRACK提高了TR分析的可及性和可重复性，同时为用户提供了灵活性。
可用性和实施方式
带有分步教程的TRACK工具包可在https://github.com/caroladam/track上免费获取。
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