Fast STR allele identification with STRait Razor 3.0. (September 2017)

• Record Type: Journal Article
• Authors: Woerner, August E.; King, Jonathan L.; Budowle, Bruce
• Is Part Of: Forensic science international. Volume 30(2017)
• Page Start: 18
• Page End: 23
• Publication Date: 2017-09
• Subjects: STRait Razor -- Short tandem repeats -- Bioinformatics -- Massively parallel sequencing -- Flanking variation; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2017.05.008
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: Fast, cross-platform allele identification. ∼660× faster than previous version. ∼60× faster than BWA Abstract: The short tandem repeat allele identification tool (STRait Razor), a program used to characterize the haplotypes of short tandem repeats (STRs) in massively parallel sequencing (MPS) data, was redesigned. STRait Razor v3.0 performs ∼660× faster allele identification than its previous version (v2s), a speedup that is largely due to a novel indexing strategy used to perform "fuzzy" (approximate) string matching of anchor sequences. Written in a portable compiled language, C++, STRait Razor v3.0 functions on all major operating systems including Microsoft Windows, and it has cross-platform multithreading support. In silico estimates of precision and accuracy of STRait Razor v3.0 were 100% in this evaluation and results were highly concordant with those of Strait Razor v2s. STRait Razor v3.0 adds several key features that simplify the haplotype reporting process, including simple filters to remove low frequency haplotypes as well as merging haplotypes within a locus encoded on opposite strands of the DNA molecule.