Description of output files.

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

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

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

Osmotic diarrhea leads to decreased phylotype richness.

<p>(<b>A</b>) Rarefaction analysis of averaged stool samples before (time-point 2, red) and during diarrhea (time-point 3, green) shows significantly decreased richness (richness time-point 2 vs. time point 3: <i>P</i> = 0.029, Student’s t-test). (<b>B</b>) Rarefaction analysis of averaged mucosa samples before (time-point 2, red) and during diarrhea (time-point 3, green) shows a trend toward but non-significant decrease in richness (richness time-point 2 vs. time point 3: <i>P</i> = 0.08 Student’s t-test). The dotted line indicates ± SEM; OTU distance = 0.03.</p

Study design.

<p>Subjects were on a free diet from day –7 to day –2 and from day 4 to day 10. From day −1 to day 0 a standardized diet was ingested. Diarrhea was induced by PEG for 3 days (day 1 to day 3). One stool sample was obtained one week before induction of diarrhea. Before the first dose of PEG a second stool sample and a mucosa sample were collected. A third stool and a second mucosa sample were taken at day three of PEG administration when diarrhea was maximally pronounced. A fourth stool sample was taken one week after withdrawal of PEG.</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

Changing taxa due to diarrhea in stool samples.

#<p>Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods.</p>*<p>(M) <i>Metastats</i>, (E) <i>edgeR</i>, (V) scoring & visualization.</p>+<p>Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score.</p

Changing taxa due to diarrhea in mucosa samples.

#<p>Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods.</p>*<p>(M) <i>Metastats</i>, (E) <i>edgeR</i>, (V) scoring & visualization.</p>+<p>Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score.</p

Consistency of measures.

<p>Congruence of <i>Metastats, edgeR</i> and <i>Viz</i> (denoted “Profile”; in at least two individuals simultaneously) for identification of significantly changing OTUs (diversity = 0.03) in stool samples (<b>A</b>) and mucosa samples (<b>B</b>).</p