refgenie

Refgenie: Genome Asset Management and Indexing System

Refgenie manages, organizes, indexes, and retrieves genome-related assets, including genome assemblies, sequence aligner indexes, and annotation files, within a standardized and reproducible repository structure.

Key Features:

• Asset Management: Organizes and retrieves genome assemblies, sequence aligner indexes, and annotation files using a structured genome folder architecture.
• Indexing and Sharing: Generates and distributes indexed genome assemblies to support collaborative and reproducible analyses.
• Custom Asset Creation: Builds assets for custom genome assemblies to support project-specific genomic references.
• Standardized Genome Structure: Enables programmatic switching between genome assemblies through a consistent directory schema.
• RESTful API Access: Provides server-based programmatic access to genome resources for integration into computational workflows.

Scientific Applications:

• High-Throughput Sequencing Analysis: Supports workflows from sequence alignment to functional genomics by managing indexed reference genomes and associated assets.
• Collaborative Genomics: Facilitates sharing of indexed genome resources to improve reproducibility and multi-user research coordination.

Methodology:

Refgenie maintains a structured repository of genome assemblies and derived assets, automates asset indexing and retrieval, and supports local and remote access through a standardized architecture and RESTful API to ensure reproducible genome resource management.