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

Abstract

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.

The concordance of length- and sequence-based STRs used in forensic markers with guidance for practice

“…As commercial NGS kits contained more markers, none of the recent commercial CE kits can share 100% comparable markers. The Powerplex® Fusion 6C system (Promega) or Verifiler TM Furthermore, two or more different analysis tools were recommended for forensic sequencing data to minimize errors in data interpretation (11).…”

“…For Y- STRs, we recommended the Powerplex Y23 system (Promega) or the Yfiler TM Plus amplification kit (Applied Biosystem) that contained 19 comparable Y-STRs. Furthermore, two or more different analysis tools were recommended for forensic sequencing data to minimize errors in data interpretation (11).…”

“…Furthermore, two or more different analysis tools were recommended for forensic sequencing data to minimize errors in data interpretation (11).…”

“…However, both open source and commercial software were available as alternative analysis tools. Each software was based on a different way to extract the STR sequence from raw files and provided distinct advantages (11). For example, STRinNGS v2.0 was a free alternative software operated on Docker (12).…”

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

“…In April 2019 the STRAND ( S hort T andem R epeat: A lign, N ame, D efine) Working Group was formalized [ 355 ] to consider several possible approaches to sequence-based STR nomenclature that have been proposed [ 356 , 357 ]. An overview of software options has been provided for analysis of forensic sequencing data [ 358 ]. Some recent published options include STRinNGS [ 359 ], STRait Razor [ 360 ], ArmedXpert tools MixtureAce and Mixture Interpretation to analyze MPS-STR data [ 361 ], and STRsearch for targeted profiling of STRs in MPS data [ 362 ].…”