genomon

Genomon is a modular, open-source software framework for cancer genome analysis, designed to identify somatic mutations from paired tumor-normal sequencing data. It provides end-to-end workflows that go from raw sequencing reads to annotated variant calls and interpretable reports, with emphasis on distinguishing somatic events from germline variation. The platform supports data from whole-exome, whole-genome, and targeted sequencing, and can be configured to run through multiple pipeline stages, including somatic single-nucleotide variant and insertion-deletion calling, copy-number alteration analysis, and, in its related components, structural variant detection.

Genomon emphasizes reproducibility and extensibility. It offers containerized or configurable deployments, documentation for workflow customization, and integration with common annotation resources. A subproject, GenomonSV, focuses specifically on detecting structural variants in cancer genomes. The project is community-driven and has its origins in Japan, with contributions from academic and research institutions. It has been described in scientific literature as a flexible framework that enables researchers to compare and combine results from different mutational callers within a single workflow.

Users typically operate Genomon on Linux systems, often within a research computing environment or cloud infrastructure, and they rely on standard bioinformatics tools for alignment, preprocessing, and downstream analysis. Genomon continues to evolve with updates that address new sequencing technologies and analytical challenges in oncology research. See also: GenomonSV, Genomon2, somatic mutation analysis in cancer genomes. External resources include the project website and public code repositories.