Gigwa

Gigwa provides scalable storage, querying, filtering, visualization, and export of large genotyping datasets to support genome-wide analyses of genetic variation from next-generation sequencing.

Key Features:

• Data management and scalability: Uses MongoDB for data storage to handle large-scale genotyping datasets and supports multiple database backends with local or online deployment.
• Data import and export: Accepts VCF, PLINK, and HapMap input formats and exports to a range of common genotype data formats.
• Advanced filtering and visualization: Provides advanced filtering by variant features, functional annotations, and specific genotype patterns, and offers visualization outputs such as density charts.
• Interoperability and connectivity: Implements GA4GH and BrAPI RESTful APIs and connects with third-party tools including FlapJack and IGV.
• Species-agnostic analysis: Supports species-agnostic analyses of genotyping data originating from next-generation sequencing platforms.

Scientific Applications:

• Genome structure and evolution: Enables analysis of genome structure and evolutionary patterns through filtered genotype and variant annotation queries.
• Population genetics and dynamics: Supports population genetics and population dynamics investigations by querying genotype patterns across samples.
• Ecological adaptation and diversity: Facilitates studies of ecological adaptation and genetic diversity via variant annotation and genotype pattern filtering.
• Breeding and health-related genetics: Supports breeding program analyses and health-related genetic investigations by exporting and interoperating genotype datasets with tools and APIs such as BrAPI.

Methodology:

Data are stored in MongoDB; imports and exports use VCF, PLINK, and HapMap formats; querying uses advanced filters on variant features, functional annotations, and genotype patterns; interoperability is provided via RESTful GA4GH and BrAPI APIs; visualization includes density charts and connections to FlapJack and IGV.