Figure 1.
The SIMPLEX analysis pipeline contains five major steps (blue boxes), which are further divided into several components. Mandatory components are depicted in black, optional in gray. The first step of the pipeline includes calculations of quality statistics on raw and processed reads, and applies filters and trimmers on sequenced reads (quality report). Afterwards, the pipeline aligns the processed reads to a reference genome (sequence alignment), performs alignment statistics and region filtering (alignment statistics), and detects variants resulting in a list of potential disease driver candidates (variant detection). Output files can be visualized using standard genome viewers. At the end, the pipeline automatically annotates variants, generates a detailed summary report, and combines calculated results including key figures in a structured way (annotation & summary).
Table 1.
Mandatory pipeline parameters.
Table 2.
Description of output files.
Table 3.
Detailed results of SIMPLEX evaluation.
Table 4.
Runtime summary for Kabuki syndrome study.
Table 5.
Comparison of exome analysis tools.