CoverView: a sequence quality evaluation tool for next generation sequencing data.
MetadataShow full item record
Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review. It also provides an interactive graphical user interface (GUI) that can be opened in a web browser and allows intuitive exploration of results. We have integrated CoverView into our accredited clinical cancer predisposition gene testing laboratory that uses the TruSight Cancer Panel (TSCP). CoverView has been invaluable for optimisation and quality control of our testing pipeline, providing transparent, consistent quality metric information and automatic flagging of regions that fall below quality thresholds. We demonstrate this utility with TSCP data from the Genome in a Bottle reference sample, which CoverView analysed in 13 seconds. CoverView uses data routinely generated by NGS pipelines, reads standard input formats, and rapidly creates easy-to-parse output text (.txt) files that are customised by a simple configuration file. CoverView can therefore be easily integrated into any NGS pipeline. CoverView and detailed documentation for its use are freely available at github.com/RahmanTeamDevelopment/CoverView/releases and www.icr.ac.uk/CoverView.
Version of record
Quality Sequencing Minimimum
depth of coverage
License start date
Wellcome Open Res, 2018, 3 pp. 36 - ?
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/
Showing items related by title, author, creator and subject.
The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing data quality assurance. Mahamdallie, S; Ruark, E; Yost, S; Münz, M; Renwick, A; Poyastro-Pearson, E; Strydom, A; Seal, S; Rahman, N (2018)Next generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated. Three primary metrics are used ...
Online dose reconstruction for tracked volumetric arc therapy: Real-time implementation and offline quality assurance for prostate SBRT. Kamerling, CP; Fast, MF; Ziegenhein, P; Menten, MJ; Nill, S; Oelfke, U (2017-11)PURPOSE: Firstly, this study provides a real-time implementation of online dose reconstruction for tracked volumetric arc therapy (VMAT). Secondly, this study describes a novel offline quality assurance tool, based on ...
Empowerment in adolescents and young adults with cancer: Relationship with health-related quality of life. Kaal, SEJ; Husson, O; van Duivenboden, S; Jansen, R; Manten-Horst, E; Servaes, P; Prins, JB; van den Berg, SW; van der Graaf, WTA (2017-10-15)BACKGROUND: The difficulties adolescents and young adults (AYAs) encounter during a cancer experience may result in a reduction in or absence of empowerment. The aims of the current study were to assess levels of empowerment ...