MultiQC Plugin for Duplex Sequencing

OVERVIEW

This project focused on improving quality-control reporting for duplex sequencing workflows. The work involved extending metric calculation, improving MultiQC integration and strengthening the reproducibility of the reporting pipeline.

THE PROBLEM

The existing reporting workflow required improvements in metric coverage, output consistency and integration with the broader sequencing pipeline. The goal was to make quality-control results easier to generate, validate and interpret.

APPROACH

As part of the team, we improved the duplex sequencing quality-control workflow across metric calculation, MultiQC reporting, reproducibility and pipeline integration. My contributions focused on refactoring the calculate-duplex-metrics repository, improving the command-line interface and help documentation, expanding and restructuring quality metric calculations, and supporting the standardised output required for MultiQC integration. I also contributed to testing and reproducibility improvements to make the workflow more robust and easier to maintain.

KEY OUTCOMES

The project expanded quality metric coverage, improved the structure and flexibility of the reporting workflow, and introduced new MultiQC visualisations for clearer quality-control reporting. Reproducibility and maintainability were also strengthened through Docker support, improved installation workflows, and automated testing.