Fast STR allele identification with STRait Razor 3.0

August E Woerner; Jonathan L King; Bruce Budowle

doi:10.1016/j.fsigen.2017.05.008

Fast STR allele identification with STRait Razor 3.0

Forensic Sci Int Genet. 2017 Sep:30:18-23. doi: 10.1016/j.fsigen.2017.05.008. Epub 2017 Jun 1.

Authors

August E Woerner¹, Jonathan L King², Bruce Budowle³

Affiliations

¹ Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA. Electronic address: August.Woerner@unthsc.edu.
² Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
³ Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.

PMID: 28605651
DOI: 10.1016/j.fsigen.2017.05.008

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.

Keywords: Bioinformatics; Flanking variation; Massively parallel sequencing; STRait Razor; Short tandem repeats.

Publication types

Evaluation Study

MeSH terms

Algorithms
Alleles*
Haplotypes*
High-Throughput Nucleotide Sequencing
Humans
Microsatellite Repeats*
Software*