About SRAKE - SRA Knowledge Engine

Pronunciation: Like Japanese sake (酒) — “srah-keh”

What is SRAKE?

SRAKE (SRA Knowledge Engine) is a blazing-fast, memory-efficient tool for processing and querying NCBI SRA (Sequence Read Archive) metadata. Built with a zero-copy streaming architecture, SRAKE can process multi-gigabyte compressed archives without intermediate storage, making it ideal for bioinformatics workflows and large-scale genomic data analysis.

Key Features

• Streaming Architecture: Process 14GB+ compressed archives without intermediate storage
• High Performance: 20,000+ records/second throughput with concurrent processing
• Memory Efficient: Constant < 500MB memory usage regardless of file size
• Resume Capability: Intelligent resume from interruption point with progress tracking
• SQLite Backend: Optimized schema with full-text search and smart indexing
• Quality-Controlled Search: Multiple search modes with similarity thresholds and confidence scoring
• Vector Embeddings: Semantic search using SapBERT for biomedical concepts

Project Status

⚠️ Important Notice: SRAKE is a hackathon project developed at BioHackathon 2025, Mie, Japan. It is currently in pre-alpha stage and not production-ready. Please treat it as an experimental tool for exploration and testing only.

Contributing

Bug reports and feature requests are welcome! Please visit our GitHub repository to contribute or report issues.

License

SRAKE is released under the MIT License. See the LICENSE file for details.