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MultiQC: Summarize analysis results for multiple tools and samples in a single report

Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller. Bioinformatics (2016)

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Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.

Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.

Availability: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports available at

This is an Open Access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.