GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction

Genome annotations have become increasingly complex with the discovery of diverse regulatory elements and transcript variants, posing growing challenges for efficient data querying and storage. Existing tools often show performance bottlenecks when processing large-scale annotation files, especially for region-based searches and hierarchical feature extraction. Leveraging Rust's advantages in execution speed, memory safety, and multithreading offers a promising path toward scalable solutions for genome annotation access.

We present GFFx, a Rust-based toolkit for high-performance access to GFF annotation files. It employs a compact, model-aware indexing system and memory-mapped I/O to enable fast random access with minimal overhead. Benchmarks across multiple genomes show 10-80 times faster ID-based extraction, 20-60 times faster region retrieval, and 7-14 times faster coverage profiling than existing tools, while maintaining low memory use and small index size.

GFFx offers a lightweight and scalable infrastructure for efficient genome annotation access and quantitative analysis. By combining Rust's performance and safety with an extensible design, it provides a robust foundation for large-scale and multi-omics workflows.