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bioRxiv · 10.1101/2020.11.13.363689

Trecode: a FAIR eco-system for the analysis and archiving of omics data in a combined diagnostic and research setting

Kerstens, H.·Hehir-Kwa, J.·van de Geer-de Jong, E.·van Run, C.·Verwiel, E.·van der Leest, D.·Tops, B.·Kemmeren, P.
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Abstract

MotivationThe increase in speed, reliability and cost-effectiveness of high-throughput sequencing has led to the widespread clinical application of genome (WGS), exome (WXS) and transcriptome analysis. WXS and RNA sequencing is now being implemented as standard of care for patients and for patients included in clinical studies. To keep track of sample relationships and analyses, a platform is needed that can unify metadata for diverse sequencing strategies with sample metadata whilst supporting automated and reproducible analyses. In essence ensuring that analysis is conducted consistently, and data is Findable, Accessible, Interoperable and Reusable (FAIR). ResultsWe present "Trecode", a framework that records both clinical and research sample (meta) data and manages computational genome analysis workflows executed for both settings. Thereby achieving tight integration between analyses results and sample metadata. With complete, consistent and FAIR (meta) data management in a single platform, stacked bioinformatic analyses are performed automatically and tracked by the database ensuring data provenance, reproducibility and reusability which is key in worldwide collaborative translational research. Availability and implementationThe Trecode data model, codebooks, NGS workflows and client programs are currently being cleared from local compute infrastructure dependencies and will become publicly available in spring 2021. Contactp.kemmeren@prinsesmaximacentrum.nl

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Kerstens, H., Hehir-Kwa, J., van de Geer-de Jong, E., van Run, C., Verwiel, E., van der Leest, D., Tops, B., Kemmeren, P.. 2020-11-16. Trecode: a FAIR eco-system for the analysis and archiving of omics data in a combined diagnostic and research setting. https://doi.org/10.1101/2020.11.13.363689

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