GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.
We are grateful to the anonymous reviewers for their suggestions and comments. This research was funded by US National Institutes of Health awards to R.M.L. (K99HG009532) and A.R.Q. (R01HG006693, R01GM124355, U24CA209999).
Integrated supplementary information
Cell line, tissue, and trait names from Figure 1; accession numbers from Figures 1 and 2 and Supplementary Figure 2.