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bioRxiv · 10.1101/2025.09.19.676923

LCR-modules: a collection of workflows for cancer genome analysis

Dreval, K.·Hilton, L. K.·Grande, B. M.·Coyle, K. M.·Cruz, M.·Gillis, S.·Pararajalingam, P.·Rushton, C. K.·Shaalan, H.·Thomas, N.·Winata, H.·Wong, J.·Yiu, J.·Steidl, C.·Scott, D. W.·Morin, R. D.
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Abstract

The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10,800 samples.

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Dreval, K., Hilton, L. K., Grande, B. M., Coyle, K. M., Cruz, M., Gillis, S., Pararajalingam, P., Rushton, C. K., Shaalan, H., Thomas, N., Winata, H., Wong, J., Yiu, J., Steidl, C., Scott, D. W., Morin, R. D.. 2025-09-24. LCR-modules: a collection of workflows for cancer genome analysis. https://doi.org/10.1101/2025.09.19.676923

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