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

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

doi:10.1016/j.fsigen.2021.102463

Cited by 20 publications

(24 citation statements)

References 39 publications

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“…This hidden variation, along with the enhanced multiplex capabilities of NGS platforms over CE and Sanger sequencing, greatly expands upon the resolution and discriminatory power of current STR panels [7,11,13,15]. Despite continued efforts focused on the development of streamlined, forensic-specific workflows [16,17] and data analysis software [18,19], widespread adoption of sequence-based STR typing has been hindered by the relatively high startup fees, involved workflows, and steep learning curves associated with NGS [20,21]. Most forensic laboratories would be unable to allocate the funds needed to purchase and validate an NGS platform while maintaining current STR typing workflows.…”

Section: Introductionmentioning

confidence: 99%

Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

Hall

Kesharwani

Phillips

et al. 2022

Forensic Science International: Genetics

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Section: Introductionmentioning

confidence: 99%

Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

Hall

Kesharwani

Phillips

et al. 2022

Forensic Science International: Genetics

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“…This software, designed to analyze reads from sequenced amplicons targeting STRs, was first published in 2013. Its evolution went through iterations from STRait Razor [11], v2.0 [12], v2s [13], v3.0 [14], and STRait Razor Online (SRO) [15] improving its processing speeds and output files, extending its analysis to the flanking regions and providing secondary analysis tools, such as additional workbooks for visual interpretation of the data using histograms and reporting sequence alleles following the International Society for Forensic Genetics (ISFG) early considerations [37].…”

Section: Strait Razormentioning

confidence: 99%

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

Huszar

Gettings

Vallone

2021

Genes

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The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.

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“…TR alleles can be reported as sequence variants or haplotypes using next generation sequencing (NGS) technologies with higher confidence and lower cost per base pair than traditional methods (Slatko et al 2018). Bioinformatic tools have been developed to detect TR haplotypes from sequence datasets, such as STRait Razor (Woerner et al 2017; King et al 2021), HipSTR (Willems et al . 2017) and FDSTools (Hoogenboom et al 2017).…”

Section: Introductionmentioning

confidence: 99%

USAT: a Bioinformatic Toolkit to Facilitate Interpretation and Comparative Visualization of Tandem Repeat Sequences

Wang

Budowle

2022

Preprint

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Tandem repeats (TR), which are highly variable genomic variants, are widely used in individual identification, disease diagnostics and evolutionary studies. The recent advances of sequencing technologies and bioinformatic tools facilitate calling TR haplotypes. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision to characterize TR haplotypes. Analysis of the differences between or among TR haplotypes, especially at the single nucleotide level, is the focus of TR haplotype characterization. In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which includes allele size conversion, sequence comparison of haplotypes, figure plotting and comparison for allele distribution, and interactive visualization. An example application of USAT for analysis of the CODIS core STR loci with benchmarking human individuals demonstrated the capabilities of USAT. USAT has a user-friendly graphic interface and runs in all major computing operating systems at a fast speed with parallel computing enabled. In summary, USAT is able to facilitate the interpretation, visualization, and comparisons of TRs.

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

Cited by 20 publications

References 39 publications

Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

USAT: a Bioinformatic Toolkit to Facilitate Interpretation and Comparative Visualization of Tandem Repeat Sequences

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