Runtime summary for Kabuki syndrome study.

<p>Listed are overall and key runtime statistics (in hours).</p

Detailed results of SIMPLEX evaluation.

<p>Listed are key figures (in avg.) for SE and PE samples.</p

Description of output files.

<p>Listed are key intermediate and final results that are created by the pipeline.</p

Schematic overview.

<p>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).</p

Mandatory pipeline parameters.

<p>Listed are all parameters that need to be specified when starting the pipeline.</p><p>If PE data is given, the file names need to end with _R1 or _R2.</p