Fast STR allele identification with STRait Razor 3.0

Research output: Contribution to journalArticleResearchpeer-review

16 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)18-23
Number of pages6
JournalForensic Science International: Genetics
Volume30
DOIs
StatePublished - 1 Sep 2017

Fingerprint

Microsatellite Repeats
Haplotypes
Alleles
High-Throughput Nucleotide Sequencing
Computer Simulation
Language
DNA

Keywords

  • Bioinformatics
  • Flanking variation
  • Massively parallel sequencing
  • STRait Razor
  • Short tandem repeats

Cite this

@article{1ac2e91b9e854d83abcf9b1454c305eb,
title = "Fast STR allele identification with STRait Razor 3.0",
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",
author = "Woerner, {August Eric} and King, {Jonathan L.} and Bruce Budowle",
year = "2017",
month = "9",
day = "1",
doi = "10.1016/j.fsigen.2017.05.008",
language = "English",
volume = "30",
pages = "18--23",
journal = "Forensic Science International: Genetics",
issn = "1872-4973",
publisher = "Elsevier Ireland Ltd",

}

Fast STR allele identification with STRait Razor 3.0. / Woerner, August Eric; King, Jonathan L.; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 30, 01.09.2017, p. 18-23.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Fast STR allele identification with STRait Razor 3.0

AU - Woerner, August Eric

AU - King, Jonathan L.

AU - Budowle, Bruce

PY - 2017/9/1

Y1 - 2017/9/1

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Flanking variation

KW - Massively parallel sequencing

KW - STRait Razor

KW - Short tandem repeats

UR - http://www.scopus.com/inward/record.url?scp=85020461032&partnerID=8YFLogxK

U2 - 10.1016/j.fsigen.2017.05.008

DO - 10.1016/j.fsigen.2017.05.008

M3 - Article

VL - 30

SP - 18

EP - 23

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

ER -