GeniePool

GeniePool provides integrated access to Sequence Read Archive (SRA) next-generation sequencing (NGS) datasets and associated phenotypic metadata to support variant analysis and genotype–phenotype studies.

Key Features:

• Integration of Genotypic and Phenotypic Data: Integrates genotypic data with corresponding phenotypic attributes and metadata to support genotype–phenotype correlations.
• Cloud data lake storage: Stores raw NGS data downloaded from the Sequence Read Archive (SRA) in a cloud data lake for large-scale data management.
• Processing pipeline: Processes datasets using SRAtoolkit and GATK as part of the automated data processing workflow.
• RESTful API access: Exposes sample-specific information and study metadata via a RESTful API for programmatic retrieval.
• Continuous data update: Employs a continuously operating pipeline to ingest new NGS submissions from SRA and update the dataset.
• Versatile application support: Provides integrated genomic data and metadata resources to support diverse clinical and research workflows.

Scientific Applications:

• Clinical Genomics: Supports diagnostic interpretation, investigation of disease mechanisms, and treatment decision-making using integrated genotypic and phenotypic data.
• Research Endeavors: Enables large-scale studies of genotype–phenotype correlations, population genetics, variant analysis, oncology, rare diseases, and evolutionary biology using aggregated NGS datasets and metadata.

Methodology:

A continuous pipeline downloads raw NGS data from the Sequence Read Archive (SRA) into a cloud data lake and processes datasets using SRAtoolkit and GATK, with data and sample metadata exposed via a RESTful API.