Table3_TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.XLSX

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.

从DNA序列中识别串联重复（TR）变异不仅具有理论意义，亦蕴含实践价值。目前，已有生物信息学工具被开发用于检测或基因分型TR变异。然而，关于从长读长测序数据中基因分型TR等位基因的研究尚显不足，且从下一代测序数据中基因分型TR等位基因的准确性仍需提升。本文描述了一种新型算法，用于从序列比对中检索TR区域，并开发了一套名为TRcaller的软件程序，并将其整合至网络门户，以从短读长和长读长序列中，以及来自多个测序平台的全基因组或靶向序列中识别TR等位基因。所有TR等位基因均被基因分型为单倍型，且即便在DNA混合物中存在多个等位基因，稳健的等位基因也将被报告。与主流软件工具相比，TRcaller在检测TR等位基因方面能提供显著更高的准确性（在289名人类个体中超过99%），且检测速度更快（例如，对于300倍人类序列数据仅需约2秒）。网络门户已预先选择119个与法医、家系和疾病相关的TR位点。TRcaller经过验证，具有良好的可扩展性，适用于多种应用，如DNA法医和疾病诊断，并可扩展至其他领域，如育种计划。获取方式：TRcaller可通过https://www.trcaller.com/SignIn.aspx获取。