STRait Razor Online: An enhanced user interface to facilitate interpretation of MPS data

Jonathan L King; August E Woerner; Sammed N Mandape; Kapema Bupe Kapema; Rodrigo Soares Moura-Neto; Rosane Silva; Bruce Budowle

doi:10.1016/j.fsigen.2021.102463

STRait Razor Online: An enhanced user interface to facilitate interpretation of MPS data

Forensic Sci Int Genet. 2021 May:52:102463. doi: 10.1016/j.fsigen.2021.102463. Epub 2021 Jan 13.

Authors

Jonathan L King¹, August E Woerner², Sammed N Mandape³, Kapema Bupe Kapema³, Rodrigo Soares Moura-Neto⁴, Rosane Silva⁵, Bruce Budowle²

Affiliations

¹ Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. Electronic address: Jonathan.King@unthsc.edu.
² Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA; Department of Microbiology, Immunology, and Genetics, 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.
⁴ Instituto de Biologia, Universidade Federal do Rio de Janeiro, RJ, Brazil.
⁵ Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.

PMID: 33493821
DOI: 10.1016/j.fsigen.2021.102463

Abstract

Since 2013, STRait Razor has enabled analysis of massively parallel sequencing (MPS) data from various marker systems such as short tandem repeats, single nucleotide polymorphisms, insertion/deletions, and mitochondrial DNA. In this paper, STRait Razor Online (SRO), available at https://www.unthsc.edu/straitrazor, is introduced as an interactive, Shiny-based user interface for primary analysis of MPS data and secondary analysis of STRait Razor haplotype pileups. This software can be accessed from any common browser via desktop, tablet, or smartphone device. SRO is available also as a standalone application and open-source R script available at https://github.com/ExpectationsManaged/STRaitRazorOnline. The local application is capable of batch processing of both fastq files and primary analysis output. Processed batches generate individual report folders and summary reports at the locus- and haplotype-level in a matter of minutes. For example, the processing of data from ∼700 samples generated with the ForenSeq Signature Preparation Kit from allsequences.txt to a final table can be performed in ∼40 min whereas the Excel-based workbooks can take 35-60 h to compile a subset of the tables generated by SRO. To facilitate analysis of single-source, reference samples, a preliminary triaging system was implemented that calls potential alleles and flags loci suspected of severe heterozygote imbalance. When compared to published, manually curated data sets, 98.72 % of software-assigned allele calls without manual interpretation were consistent with curated data sets, 0.99 % loci were presented to the user for interpretation due to heterozygote imbalance, and the remaining 0.29 % of loci were inconsistent due to the analytical thresholds used across the studies.

Keywords: Bioinformatics; Massively parallel sequencing; Next-generation sequencing; STRait razor.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA Fingerprinting
High-Throughput Nucleotide Sequencing*
Humans
Internet
Microsatellite Repeats
Sequence Analysis, DNA
Software*
User-Computer Interface*