Outputs


Tools and Resources

OpEx

The OpEx NGS pipeline provides a fixed implementation of alignment, calling and annotation tools optimized for individual or multiple exome sequencing analysis in the research or clinical setting.

Download and documentation
Read more about OpEx on our blog

DECoN

DECoN identifies exon copy number variants (CNVs) in targeted sequencing data. DECoN is optimised for clinical utility and provides quality information and GUI visualisation to aid interpretation of results.

Download and documentation
Read more about DECoN on our blog

ICR96

ICR96 Exon CNV validation series

The ICR96 Exon CNV validation series is a sequencing dataset of 96 samples for orthogonal assessment of exon CNV calling in NGS data. It includes 66 samples with at least one validated exon CNV and 30 samples with validated negative results for exon CNVs in 26 genes.

Download and documentation
Read more about ICR96 on our blog

CoverView

CoverView is a user-friendly quality evaluation tool for NGS data. It processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics from a chromosome-level summary to per-base profiles.

Download and documentation
Read more about CoverView (and QSM) on our blog

 

 

Publications

Mahamdallie S, Ruark E, Yost S et al. The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing  data quality assurance [version 1; referees: awaiting peer review]. Wellcome Open Res 2018, 3:37 (doi: 10.12688/wellcomeopenres.14307.1)

Münz M, Mahamdallie S, Yost S et al. CoverView: a sequence quality evaluation tool for next generation sequencing data [version 1; referees: awaiting peer review]. Wellcome Open Res 2018, 3:36 (doi: 10.12688/wellcomeopenres.14306.1)

Wright CF, FitzPatrick DR, and Firth HV (2018) Paediatric genomics: diagnosing rare disease in children Nature Reviews Genetics, Published online

Mahamdallie S, Ruark E, Yost S et al. (2017) The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data [version 1: referees: 2 approved]. Wellcome Open Res 2017, 2:35 (doi: 10.12688/wellcomeopenres.11689.1)

Fowler A, Mahamdallie S, Ruark E, Seal S, Ramsey E, Clarke M, Uddin I, Wylie H, Strydom A, Lunter G, and Rahman N. (2016) Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN [version 1; referees: 2 approved]. Wellcome Open Res 2016, 1:20 (doi: 10.12688/wellcomeopenres.10069.1)

Ruark E, Münz M, Clarke M, Renwick A, Ramsay E, Elliott A, Seal S, Lunter G, and Rahman N. (2016) OpEx – a validated, automated pipeline optimised for clinical exome sequence analysisScientific Reports 2016, 6:31029 (doi:10.1038/srep31029)

 

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