TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data. Issue 10 (7th October 2020)

• Record Type: Journal Article
• Authors: Bolognini, Davide; Magi, Alberto; Benes, Vladimir; Korbel, Jan O; Rausch, Tobias
• Is Part Of: GigaScience. Volume 9:Issue 10(2020)
• Publication Date: 2020-10-07
• Subjects: long-read sequencing -- tandem repeat variation -- bioinformatics software; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giaa101
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: Tandem repeat sequences are widespread in the human genome, and their expansions cause multiple repeat-mediated disorders. Genome-wide discovery approaches are needed to fully elucidate their roles in health and disease, but resolving tandem repeat variation accurately remains a challenging task. While traditional mapping-based approaches using short-read data have severe limitations in the size and type of tandem repeats they can resolve, recent third-generation sequencing technologies exhibit substantially higher sequencing error rates, which complicates repeat resolution. Results: We developed TRiCoLOR, a freely available tool for tandem repeat profiling using error-prone long reads from third-generation sequencing technologies. The method can identify repetitive regions in sequencing data without a prior knowledge of their motifs or locations and resolve repeat multiplicity and period size in a haplotype-specific manner. The tool includes methods to interactively visualize the identified repeats and to trace their Mendelian consistency in pedigrees. Conclusions: TRiCoLOR demonstrates excellent performance and improved sensitivity and specificity compared with alternative tools on synthetic data. For real human whole-genome sequencing data, TRiCoLOR achieves high validation rates, suggesting its suitability to identify tandem repeat variation in personal genomes.