Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

Front Genet. 2013 Dec 17;4:288. doi: 10.3389/fgene.2013.00288.

Abstract

The processes of quality assessment and control are an active area of research at The Genome Analysis Centre (TGAC). Unlike other sequencing centers that often concentrate on a certain species or technology, TGAC applies expertise in genomics and bioinformatics to a wide range of projects, often requiring bespoke wet lab and in silico workflows. TGAC is fortunate to have access to a diverse range of sequencing and analysis platforms, and we are at the forefront of investigations into library quality and sequence data assessment. We have developed and implemented a number of algorithms, tools, pipelines and packages to ascertain, store, and expose quality metrics across a number of next-generation sequencing platforms, allowing rapid and in-depth cross-platform Quality Control (QC) bioinformatics. In this review, we describe these tools as a vehicle for data-driven informatics, offering the potential to provide richer context for downstream analysis and to inform experimental design.

Keywords: NGS data analysis; QC; bioinformatics tools; contamination screening; quality assessment and improvement; quality control; run statistics; sequence analysis.

Publication types

  • Review