KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis

Gupta, P.; Riehl, W. J.; Cashman, M.; Chivian, D.; Neely, C. J.; Canon, S. R.; Cottingham, R.; Henry, C.; Arkin, A. P.; Dehal, P. S.

doi:10.64898/2026.06.01.729336

bioRxiv · 10.64898/2026.06.01.729336

KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis

Gupta, P.·Riehl, W. J.·Cashman, M.·Chivian, D.·Neely, C. J.·Canon, S. R.·Cottingham, R.·Henry, C.·Arkin, A. P.·Dehal, P. S.

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Abstract

Constructing multi-step bioinformatics workflows, from read quality control through genome assembly to functional annotation, requires expertise in both biology and computational tool selection, creating a bottleneck for scalable and reproducible analysis. We present the KBase Research Agent, a multi-agent system for automating such workflows within the DOE Systems Biology Knowledgebase (KBase). Given a set of sequencing reads and a research objective, the agent constructs an analysis plan grounded in KBase documentation and a Knowledge Graph (KG) of the KBase application catalog, then selects, parameterizes, validates and executes appropriate KBase applications to carry out the workflow. The resulting analysis is preserved as a reproducible KBase Narrative. We evaluate the systems planning and execution quality against ground truth constructed from reference workflows derived from peer-reviewed Microbiology Resource Announcements. We further apply the agent to 100 previously unanalyzed bacterial isolate genomes from the JGI IMG/M database, where it autonomously performed read quality control, genome assembly, taxonomic classification with GTDB-Tk, and downstream analysis producing annotated genomes, reproducible Narratives, and draft manuscripts without human intervention. Across these experiments, the KBase Research Agent demonstrates the feasibility of domain-grounded, end-to-end scientific workflow automation in a production bioinformatics platform.

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Gupta, P., Riehl, W. J., Cashman, M., Chivian, D., Neely, C. J., Canon, S. R., Cottingham, R., Henry, C., Arkin, A. P., Dehal, P. S.. 2026-06-04. KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis. https://doi.org/10.64898/2026.06.01.729336

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