A modern, portable, and high-performance variant call database.
Project description
Phoebe
A high-performance variant call warehouse, designed for scalable storage and query of population-scale variant call data.
License
A license is required to use this software. Phoebe licenses are free for academic/research use. For more information, please contact us.
Overview
Phoebe is a system for storing, managing, and querying genomic variant data from GVCFs. It addresses the core challenges of variant warehousing:
- Data arrives in groups of single-sample files, but most queries need data organized by variant.
- Random and bulk queries of variants and samples contained in the database need to be fast, even at enormous scale.
- The system must be compatible with object storages and spot instances, with simple operation on both private HPC clusters and public clouds.
The system is exposed in Python, but most of the implementation is Rust with an emphasis on performance and portability.
The system ships with the following backends out of the box:
- local multithreaded execution
- AWS Batch
- Google Cloud Run Jobs
However, Phoebe is intentionally designed so that other backends are simple to add.
Made with ❤️ in coastal Maine.
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