AstraKit: Customizable, reproducible workflows for biomedical research and precision medicine

Abstract Motivation The success of precision medicine and biomedical research depends on the availability of efficient software solutions for processing and interpreting genetic variants, interpreting multi-omics data, and integrating drug screen analyses. However, fragmented bioinformatics tools compel researchers and clinicians to resort to error-prone manual pipelines. Results We present AstraKit, a unified KNIME workflow suite enabling end-to-end precision medicine analytics. AstraKit introduces three transformative innovations: 1) Dynamic variant interpretation with customizable annotation and filtering for disease-specific genomic contexts; 2) Multi-layered omics analyses integrating genomic, transcriptomic, and epigenetic data; and 3) Translational drug matching that correlates in vitro drug screens with clinical outcomes. Validated across oncology cohorts, AstraKit demonstrates concordance between experimental drug sensitivity and clinical outcomes, resolving discordances to uncover resistance mechanisms. By unifying variant analysis, multi-omics, and drug response modeling on a single customizable platform, AstraKit eliminates siloed workflows, accelerating biomarker validation and enabling clinicians to directly link molecular profiles to therapeutic decisions. As all AstraKit workflows are open-source and platform-independent, we provide a versatile comprehensive software suite for a multitude of tasks in bioinformatics and precision medicine. Availability and implementation The KNIME workflows are available at KNIME Hub https://hub.knime.com/bioinf_goe/spaces/Public/AstraKit~lfVsGBY2HnPYc1h1/ . The source code is available at https://gitlab.gwdg.de/MedBioinf/mtb/astrakit .