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 enable 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 support various sequencing types and integrate pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represent a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability, and have already been applied to a combination of exomes and genomes from over 10,800 samples.
Dreval et al. (Wed,) studied this question.