Precise and ultrafast tandem repeat variant detection in massively parallel sequencing reads

Abstract

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. A large number of software tools have been developed for detecting TRs. However, little study has been done to detect TR alleles from long-read sequences, and the effectiveness of detecting TR alleles from whole genome sequence (WGS) 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 to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. The results showed that TRcaller could provide substantially higher accuracy in detecting TR alleles with magnitudes faster than the mainstream software tools. TRcaller is able to facilitate scalable, accurate, and ultrafast TR allele calling from large-scale sequence datasets in various applications, such as DNA forensics, medical research, disease diagnosis, evolution, and breeding programs. AvailabilityTRcaller is available at www.trcaller.com.