GIGGLE

GIGGLE performs rapid genomic interval searches to identify and rank shared genomic loci between query features and large collections of genome interval files for large-scale comparative analyses.

Key Features:

• Scalability: Capable of handling billions of genomic intervals and indexing thousands of genome interval files for large-scale analyses.
• Speed: Executes searches at speeds reported to be more than three orders of magnitude faster than existing methods.
• Data Integration: Enables comparison of query intervals against extensive public resources including ENCODE, Roadmap Epigenomics, and GTEx.
• Significance ranking: Ranks the significance of shared genomic intervals between query features and indexed interval files to prioritize candidate loci.

Scientific Applications:

• Large-scale genomic comparisons: Compare genomic loci across local and public datasets to detect shared intervals at population or genome-wide scales.
• Public dataset cross-querying: Integrate and query local data against ENCODE, Roadmap Epigenomics, and GTEx to identify overlapping regulatory or expression-related loci.
• Hypothesis generation and validation: Rapidly generate and prioritize hypotheses about potential functional relationships by ranking shared intervals for follow-up analysis.

Methodology:

Uses a sophisticated algorithmic approach to process and compare large volumes of genomic interval data and ranks the significance of shared genomic loci between query features and thousands of genome interval files.