Developing Reliable QC at the Swedish National Genomics Infrastructure
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Good quality control procedures are essential for sequencing facilities. The SciLifeLab National Genomics Infrastructure is an accredited facility that processes thousands of samples every month, driving us to develop high-throughput QC procedures. We use a LIMS, a bespoke web system and most recently MultiQC - a tool that I have written to summarise analysis log files and produce reports that visualise key sample metrics. In this talk I describe how our different systems integrate and how we use MultiQC results for both project level reporting and long term monitoring.
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Developing Reliable QC at the Swedish National Genomics Infrastructure
- 1. High Throughput QC Quality Control at the Swedish National Genomics Infrastructure Phil Ewels @ewels @tallphil Bioinfo-Core Workshop 2017-07-24 ISMB 2017, Prague
- 2. ISO accredited facility Library preparation Sequencing Bioinfo analysis NGI stockholm
- 3. ISO accredited facility Library preparation Sequencing Bioinfo analysis “This means that our services are subject to highly stringent quality control procedures, so that you can be sure that your data is of excellent quality.” NGI stockholm
- 4. 2 x MiSeq 5 x HiSeq 2500 5 x HiSeq X10 NovaSeq RNA-Seq WG Re-Seq Targeted Re-Seq Metagenomics Others 0 2000 4000 6000 8000 10000 12000 14000 1,265 2,580 3,214 8,934 12,017 Number of Samples in 2016 1141 Gbp/day 1X Human Genome every 4 minutes NGI stockholm
- 5. QC with lots of samples Always Occasionally Automation Visualisation (spot outliers) Manual checks Validations Looking for trends Good quality control at scale is essential
- 6. QC Automation All sample metadata in a database Genomics Status OrderPortal
- 8. QC Automation Collection + visualisation of results
- 9. QC Automation Collection + visualisation of results Genomics Status
- 10. Genomics Status
- 15. QC with lots of samples Always Occasionally Automation Visualisation (spot outliers) Manual checks Validations Looking for trends
- 16. Long term trends coming soon…
- 17. Long term trends Data available from 2253 samples, 738 reports Choose a plot type1 Select data2 Data HistogramReport plot Compare DataData Trend
- 18. Long term trends Data available from 2253 samples, 738 reports Select samples2 Choose a plot type1 Data Trend + Add Filter Metadata field: [ select value ] Minimum: Maximum [ 837 samples ] Date: 2017.01.01 - 2017.03.01 Application Type: WGS
- 19. Long term trends Data available from 2253 samples, 738 reports Select samples2 Choose a plot type1 Data Trend [ 837 samples ] Plot data3 Picard: % Dups Qualimap: > 30X [ add data ]
- 20. • Each lab technique has a protocol • Changes require validation • Internal audits • Horizontal (one step) • Vertical (one sample) NGI stockholm Validations In-depth reproducibility checks stockholm uppsala NGI stockholm
- 21. Analysis Validation • Versioned pipeline releases • New versions require a validation test • Runs logged and reported • Continuous integration tests
- 24. Conclusion http://github.com/SciLifeLab http://multiqc.info http://opensource.scilifelab.se NGI stockholm Phil Ewels phil.ewels@scilifelab.se ewels tallphil Acknowledgements Max Käller Rickard Hammarén Denis Moreno Francesco Vezzi NGI Stockholm Genomics Applications Development Group