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BioMed Research International
Volume 2013, Article ID 865181, 4 pages
Research Article

QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data

1Department of Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
2Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA

Received 13 September 2013; Accepted 15 October 2013

Academic Editor: Zhongming Zhao

Copyright © 2013 Bingshan Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Background. Next generation sequencing (NGS) is being widely used to identify genetic variants associated with human disease. Although the approach is cost effective, the underlying data is susceptible to many types of error. Importantly, since NGS technologies and protocols are rapidly evolving, with constantly changing steps ranging from sample preparation to data processing software updates, it is important to enable researchers to routinely assess the quality of sequencing and alignment data prior to downstream analyses. Results. Here we describe QPLOT, an automated tool that can facilitate the quality assessment of sequencing run performance. Taking standard sequence alignments as input, QPLOT generates a series of diagnostic metrics summarizing run quality and produces convenient graphical summaries for these metrics. QPLOT is computationally efficient, generates webpages for interactive exploration of detailed results, and can handle the joint output of many sequencing runs. Conclusion. QPLOT is an automated tool that facilitates assessment of sequence run quality. We routinely apply QPLOT to ensure quick detection of diagnostic of sequencing run problems. We hope that QPLOT will be useful to the community as well.