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STRait Razor Online: An enhanced user interface to facilitate interpretation of MPS data
- Source :
- Forensic Science International: Genetics. 52:102463
- Publication Year :
- 2021
- Publisher :
- Elsevier BV, 2021.
-
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.
- Subjects :
- 0301 basic medicine
FASTQ format
Computer science
computer.software_genre
Pathology and Forensic Medicine
User-Computer Interface
03 medical and health sciences
0302 clinical medicine
Software
Genetics
Humans
030216 legal & forensic medicine
Internet
Interpretation (logic)
Information retrieval
Massive parallel sequencing
business.industry
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
DNA Fingerprinting
030104 developmental biology
Batch processing
Table (database)
Compiler
User interface
business
computer
Microsatellite Repeats
Subjects
Details
- ISSN :
- 18724973
- Volume :
- 52
- Database :
- OpenAIRE
- Journal :
- Forensic Science International: Genetics
- Accession number :
- edsair.doi.dedup.....a0ab0053808a7e31e1eb455ff527e17a