Citation

If gffbase contributes to your research, please cite it.

Chao, K.-H. (2026). GFFBase: Rust-accelerated GFF3/GTF parser with a DuckDB-backed storage engine and zero-copy PyArrow interface (Version 0.2.0) [Computer software]. https://github.com/Kuanhao-Chao/gffbase

BibTeX

@software{chao_gffbase_2026,
  author  = {Chao, Kuan-Hao},
  title   = {{GFFBase}: Rust-accelerated GFF3/GTF parser with a
             DuckDB-backed storage engine and zero-copy PyArrow interface},
  year    = 2026,
  version = {0.2.0},
  url     = {https://github.com/Kuanhao-Chao/gffbase},
}

The repository also ships a CITATION.cff, so GitHub's "Cite this repository" button produces an up-to-date reference without anyone maintaining a second copy by hand. Per-version DOIs are tracked on the releases page.

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Please also cite what gffbase is built on

gffbase is a successor to gffutils and reuses its API, its test corpus and its semantics. If you are porting from it, cite it too:

Dale, R. gffutils: a Python package for working with GFF and GTF files. https://github.com/daler/gffutils

The storage engine and the columnar interface are likewise other people's work:

• DuckDB — Raasveldt, M. & Mühleisen, H. (2019). DuckDB: an Embeddable Analytical Database. SIGMOD.
• Apache Arrow — https://arrow.apache.org/

And cite the annotation you used

A result computed from GENCODE, RefSeq, MANE or CHESS depends on that annotation as much as on the software that read it. Each publisher asks to be cited; see Datasets for the sources.