FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

Abstract

Summary: FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data.

Availability and implementation: FQC is implemented in Python 3 and Javascript, and is maintained under an MIT license. Documentation and source code is available at: https://github.com/pnnl/fqc .

Contact: joseph.brown@pnnl.gov.

Fig. 1

The FQC dashboard. (A) Tab navigation with the metric name displayed on the tab and status of the metric as determined by FastQC. (B) Dropdown menus of the groups (in this example, a group represents a flow cell) and biological samples within a group available for viewing. (C) Plot tabs enable switching between multiple plots (R1 and R2 reads in this example) within a given quality metric. (D) 96-well reagent plate heatmap with positive controls encircled in red; this example shows positive control sample bleed-over into neighboring plate wells. (E) Read abundance values across a reagent plate showing potential dispensing robot failure after column 8. (F) A Lorenz curve showing the distribution of on-target reads across sequence barcodes. A live FQC example site is available at: https://pnnl.github.io/fqc/