New tool for sequencing quality control

The National Genomics Infrastructure, NGI, at SciLifeLab is responsible for sequencing a large number of projects for users across Sweden. A new tool, published in Bioinformatics by Phil Ewels and colleagues at the NGI, allows the unit and users to summarize analysis results for an entire project in a single report.

Quality control is critical for anyone involved in next generation sequencing research. Analysis pipelines, including the best-practice pipelines used at the NGI, typically produce log files giving a summary of their analysis. Checking these numbers manually is very time consuming and prone to errors. The new tool; MultiQC, works by scanning results directories and collecting log files. It summarises this information in a single report describing all samples and all bioinformatics tools. This allows fast interpretation of the pipeline results and highlights any anomalous samples.

“At the NGI, we use these reports to check our QC criteria before delivering data.” Phil Ewels says. “Other people have used MultiQC to compare analysis methods or characterise large projects with many samples. The tool is quickly gaining popularity, with the manuscript already the 19th most shared article from Bioinformatics.”

The program has been published in Bioinformatics and can be downloaded from or the SciLifeLab Open Source portal:


Last updated: 2016-06-29

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