Tools and Resources
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.
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.
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 analysis. Scientific Reports 2016, 6:31029 (doi:10.1038/srep31029)