Report Templates

Overview

FastQC supports multiple HTML report templates via the --template / -t CLI flag. This works like MultiQC's template system: the default template produces the familiar FastQC report, while alternative templates can change the layout, styling, and chart format without affecting the analysis.

fastqc --template modern sample.fastq.gz

Available templates

classic (default)

The original FastQC report layout. Produces byte-identical HTML to Java FastQC, with PNG charts embedded as base64 data URIs and the same fixed sidebar + main content layout.

This is the default when --template is not specified.

modern

A redesigned report layout ported from upstream PR #161, inspired by fastqc-viz. Key features:

• Responsive sidebar — sticky sidebar with flexbox layout, mobile-friendly hamburger menu (pure CSS, no JavaScript)
• Inline SVG charts — charts are embedded as optimised inline SVG instead of PNG, giving crisp rendering at any zoom level
• SVG status icons — Material Design pass/warn/fail icons replace the PNG icons, with styled text badges in the sidebar
• Help text accordions — each module has a CSS-only toggle to show/hide its help documentation inline
• New FastQC logo — a refreshed SVG logo used in the sidebar and mobile navigation
• Print-friendly — CSS print styles for PDF export

Text output (fastqc_data.txt, summary.txt) is identical regardless of which template is used. Only the HTML report and the icons in the zip archive differ.

SVG optimisations

The modern template applies several post-processing optimisations to the inline SVGs to keep file sizes small:

• CSS classes — repeated attributes like shape-rendering and font-family are moved to a <style> block
• Attribute shortening — verbose style="fill:rgb(...);stroke:none" replaced with fill="rgb(...)"
• Lines → polylines — consecutive same-colour line segments in data series are merged into single <polyline> elements
• Rect run-length encoding — adjacent same-colour rectangles (e.g. in the per-tile quality heatmap) are merged into wider rectangles

These optimisations reduce the modern template's file size to roughly 60% of the classic template, and to around 13% of the classic size when gzip-compressed (SVG text compresses far better than base64-encoded PNGs).

File size comparison

Example on a 27M-read FASTQ file: