QPLOT: A quality assessment tool for next generation sequencing data

Bingshan Li, Xiaowei Zhan, Mary Kate Wing, Paul Anderson, Hyun Min Kang, Goncalo R. Abecasis

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number865181
JournalBioMed Research International
Volume2013
DOIs
StatePublished - Dec 16 2013

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Fingerprint Dive into the research topics of 'QPLOT: A quality assessment tool for next generation sequencing data'. Together they form a unique fingerprint.

  • Cite this