CAMP: a modular metagenomics analysis system for integrated multistep data exploration
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1 March 2026Oxford University Press
NAR Genomics and Bioinformatics
2026#8Issue 1
Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.
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Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, 10065, NY, United States
Department of Systems and Computational Biomedicine, Weill Cornell Medicine of Cornell University, 10065, NY, United States
Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 90033, CA, United States
Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, 30-387, Poland
Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, São Paulo, 05508-900, Brazil
Natural Resource Ecology Laboratory, Colorado State University, 80521, CO, United States
Two Frontiers Project, 80521, CO, United States
Broad Institute of MIT and Harvard, 02142, MA, United States
Mathematics Institute, University of Warwick, Coventry, CV4 7AL, United Kingdom
Nazarbayev Intellectual School of Physics and Math, Almaty, 050000, Kazakhstan
School of Molecular and Theoretical Biology, Tartu, 51010, Estonia
Institute of Molecular Biology and Genetics, NASU, Kyiv, 03680, Ukraine
Kyiv Academic University, Kyiv, 03142, Ukraine
Taras Shevchenko National University, Kyiv, 01033, Ukraine
ETH Zurich, Zurich, 8092, Switzerland
Biotia, 11101, NY, United States
GeoSeeq Foundation, 11101, NY, United States
Department of Biology, Lund University, 223 62, Sweden
Department of Biological and Morphofunctional Sciences, College of Medicine and Biological Sciences, University of Suceava, Suceava, 720229, Romania
WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine of Cornell University, 10065, NY, United States
The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine of Cornell University, 10065, NY, United States
Englander Institute for Precision Medicine, Weill Cornell Medicine of Cornell University, 10065, NY, United States
Tri-Institutional Computational Biology & Medicine Program
Department of Systems and Computational Biomedicine
Department of Clinical Pharmacy
Małopolska Centre of Biotechnology
Department of Biochemistry
Natural Resource Ecology Laboratory
Two Frontiers Project
Broad Institute of MIT and Harvard
Mathematics Institute
Nazarbayev Intellectual School of Physics and Math
School of Molecular and Theoretical Biology
Institute of Molecular Biology and Genetics
Kyiv Academic University
Taras Shevchenko National University
ETH Zurich
Biotia
GeoSeeq Foundation
Department of Biology
Department of Biological and Morphofunctional Sciences
WorldQuant Initiative for Quantitative Prediction
The Feil Family Brain and Mind Research Institute
Englander Institute for Precision Medicine
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