Understanding Bioinformatics Workflows for NGS Analysis: Case Study with Whole-exome Sequencing Data

NGS enables the in-depth analysis of the genome and the identification and investigation of disease-associated variants–especially when workflows include target enrichment, which focuses on specific regions and enables higher throughput with greater sensitivity for rare variants. However, while the sample preparation and sequencing workflow takes only a few days, much work remains: (1) the assessment of the quality of the raw sequencing data, (2) the processing and analysis of the data, and (3) conversion of the data into readily understandable formats such as charts, tables, and graphs. This process is accomplished through bioinformatics, using a comprehensive suite of specialized tools.

 

In this presentation, the basic elements of bioinformatics will be reviewed–including specific steps such as trimming, downsampling, and alignment of the reads to the reference genome. The generation of sequencing metrics and the identification of variants will also be discussed, using a pipeline developed at Roche. This pipeline leverages open-source/third-party tools and thus is available to any bioinformatician, enabling them to evaluate the sequencing data from either pre-designed or custom panels from Roche.

 

Key highlights: