Figure 2.

An overview of the next generation sequencing (NGS) bioinformatics workflow. The NGS bioinformatics is subdivided in the primary (blue), secondary (orange) and tertiary (green) analysis. The primary data analysis consists of the detection and analysis of raw data. Then, on the secondary analysis, the reads are aligned against the reference human genome (or de novo assembled) and the calling is performed. The last step is the tertiary analysis, which includes the variant annotation, variant filtering, prioritization, data visualization and reporting. CNV—copy number variation; ROH—runs of homozygosity, VCF—variant calling format.