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Documentation

Welcome to the SRAKE (SRA Knowledge Engine) documentation! This guide will help you get started with processing NCBI SRA metadata efficiently.

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

What is SRAKE?

SRAKE (SRA Knowledge Engine) is a comprehensive tool for processing and querying NCBI SRA (Sequence Read Archive) metadata. Built with a streaming architecture, SRAKE can process large compressed archives without intermediate storage.

Key Features

Getting Started
Install and run srake in minutes
Filtering System
Process only the data you need
Resume Capability
Handle interruptions gracefully
API Reference
REST API and Go library

Features

  • Performance: Efficient record processing
  • Memory Management: Streaming architecture for large files
  • Pipeline: HTTP → Gzip → Tar → XML → Database streaming
  • Filtering: Filter by taxonomy, organism, platform, and more
  • Resume Support: Recovery from interruptions
  • Search: Full-text search with SQLite backend

Quick Example 

# Install SRAKE (SRA Knowledge Engine)
go install github.com/nishad/srake/cmd/srake@latest

# Ingest SRA metadata with SRAKE
srake ingest --file archive.tar.gz \
  --taxon-ids 9606 \
  --platforms ILLUMINA \
  --strategies RNA-Seq

# Search the database
srake search "homo sapiens" --limit 10

# Start SRAKE API server
srake server --port 8080