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Hydra-genetics, a modular framework for bioinformatics pipeline development
Uppsala University, Clinical Genomics Uppsala, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala, Sweden.
Uppsala University, Clinical Genomics Uppsala, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala, Sweden.
Uppsala University, Clinical Genomics Uppsala, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala, Sweden.
University Hospital of Umeå, Clinical Genetics, Laboratory Medicin, Umeå, Sweden; Umeå universitet, Clinical Genomics Umeå, Science for Life Laboratory, Department of Medical Biosciences/Pathology, Umeå, Sweden.
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2024 (English)In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 32, no Suppl. 1, p. 675-676, article id P18.093.AArticle in journal, Meeting abstract (Other academic) Published
Abstract [en]

Background: Processing information from massively parallel sequencing/next-generation sequencing (NGS) data involves several steps that transform millions of rows of input data into more accessible genetic information. The combination of bioinformatics tools that extract all requested information for a particular clinical/research application, how they are tuned and the order in which they are executed constitute a bioinformatics pipeline. Software is often reused in several pipelines and regularly updated. For clinically validated NGS pipelines it may be challenging when individual components of several pipelines needs updating or when tools are replaced with new applications.

Methods: The Hydra-genetics framework takes advantage of version controlled Snakemake modules. Pipeline steps are split into modules that can be configured and tested individually. The modules can be combined to build complete bioinformatics analyses, or be added to existing pipelines. All modules are subjected to extensive testing to ensure that new releases do not unexpectedly break existing pipelines or deviate from guidelines and best practices on how to write code.

Results: Bioinformaticians from five Genomics Medicine Sweden centers used Hydra-genetics to develop the bioinformatics pipeline for the comprehensive solid tumor panel, GMS560. The pipeline analyses tumor DNA and/or RNA data and generates information on genetic variation including complex biomarkers such as tumor mutation burden and microsatellite instability. It is validated and in clinical use.

Conclusions: The Hydra-genetics framework provides a platform for structured bioinformatics pipeline development and facilitates joint development projects involving multiple partners. It makes clinical pipeline development easier, faster and more structured.

Place, publisher, year, edition, pages
Nature Portfolio , 2024. Vol. 32, no Suppl. 1, p. 675-676, article id P18.093.A
National Category
Medical Genetics and Genomics
Identifiers
URN: urn:nbn:se:oru:diva-112062ISI: 001147414903291OAI: oai:DiVA.org:oru-112062DiVA, id: diva2:1842242
Conference
56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, Scotland, June 10-13, 2023
Available from: 2024-03-04 Created: 2024-03-04 Last updated: 2025-02-10Bibliographically approved

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Lindqvist, Mårten

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