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Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application

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Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’
Abstract
Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background. We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis. Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data.
Keywords
MPS, NGS, STR, Forensic loci, Illumina, MiSeq, GENOMES, QUALITY

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MLA
Van Neste, Christophe, Yannick Gansemans, Dieter De Coninck, et al. “Forensic Massively Parallel Sequencing Data Analysis Tool: Implementation of MyFLq as a Standalone Web- and Illumina BaseSpace®-application.” FORENSIC SCIENCE INTERNATIONAL-GENETICS 15 (2015): 2–7. Print.
APA
Van Neste, C., Gansemans, Y., De Coninck, D., Van Hoofstat, D., Van Criekinge, W., Deforce, D., & Van Nieuwerburgh, F. (2015). Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application. FORENSIC SCIENCE INTERNATIONAL-GENETICS, 15, 2–7.
Chicago author-date
Van Neste, Christophe, Yannick Gansemans, Dieter De Coninck, David Van Hoofstat, Wim Van Criekinge, Dieter Deforce, and Filip Van Nieuwerburgh. 2015. “Forensic Massively Parallel Sequencing Data Analysis Tool: Implementation of MyFLq as a Standalone Web- and Illumina BaseSpace®-application.” Forensic Science International-genetics 15: 2–7.
Chicago author-date (all authors)
Van Neste, Christophe, Yannick Gansemans, Dieter De Coninck, David Van Hoofstat, Wim Van Criekinge, Dieter Deforce, and Filip Van Nieuwerburgh. 2015. “Forensic Massively Parallel Sequencing Data Analysis Tool: Implementation of MyFLq as a Standalone Web- and Illumina BaseSpace®-application.” Forensic Science International-genetics 15: 2–7.
Vancouver
1.
Van Neste C, Gansemans Y, De Coninck D, Van Hoofstat D, Van Criekinge W, Deforce D, et al. Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application. FORENSIC SCIENCE INTERNATIONAL-GENETICS. 2015;15:2–7.
IEEE
[1]
C. Van Neste et al., “Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application,” FORENSIC SCIENCE INTERNATIONAL-GENETICS, vol. 15, pp. 2–7, 2015.
@article{5805187,
  abstract     = {Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background.
We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis.
Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data.},
  author       = {Van Neste, Christophe and Gansemans, Yannick and De Coninck, Dieter and Van Hoofstat, David and Van Criekinge, Wim and Deforce, Dieter and Van Nieuwerburgh, Filip},
  issn         = {1872-4973},
  journal      = {FORENSIC SCIENCE INTERNATIONAL-GENETICS},
  keywords     = {MPS,NGS,STR,Forensic loci,Illumina,MiSeq,GENOMES,QUALITY},
  language     = {eng},
  pages        = {2--7},
  title        = {Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application},
  url          = {http://dx.doi.org/10.1016/j.fsigen.2014.10.006},
  volume       = {15},
  year         = {2015},
}

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