Encode Toolkit

ENCODE Toolkit is an open-source genomics research infrastructure designed for seamless integration with Claude, enabling users to search, analyze, and cross-reference data from 14 major genomics databases. It offers 20 live API tools, 47 guided workflow skills, and 7 analysis pipelines to automate and streamline bioinformatics and data analysis tasks such as querying ENCODE, GWAS, ClinVar, GTEx, JASPAR, and more. It is particularly useful for biomedical researchers, bioinformaticians, and data scientists working with multi-omic datasets and publication-ready methods.