plantcad/opengenome2-metagenomes-plantcad2-c4096

OpenGenome2 Metagenomes PlantCAD2 Subset (4096bp)

This dataset is a curated subset of arcinstitute/opengenome2 designed for comparative spectral analysis with plant genomic data.

Dataset Description

Sequences were randomly sampled from OpenGenome2, filtered and truncated to match the sample sizes per split of the plantcad/Angiosperm_65_genomes_8192bp dataset.

Processing Steps

1. Streaming: Records were streamed from the metagenomes subfolder (json/pretraining_or_both_phases/metagenomes) of OpenGenome2
2. Shuffling: Applied shuffle with buffer size of 10,000 for random sampling
3. Filtering: Sequences shorter than 4096bp were excluded
4. Truncation: Sequences ≥4096bp were truncated to exactly 4096bp
5. Sampling: Collected samples to match PlantCAD split sizes

Split Sizes

Split	Number of Examples
train	2,638,656
validation	1,000
test	1,000

Note: there are only 1,000 samples in the validation and test splits of the OpenGenome2 Metagenomes data as opposed to 329,832 for those same splits in the PlantCAD2 data.

Sequence Length

All sequences are exactly 4096 base pairs.

Source Dataset

OpenGenome2 is a database of nearly 9 trillion base pairs of curated DNA from across all domains of life, used to train Evo 2 models. Please refer to the Evo 2 preprint for further details.

Usage

from datasets import load_dataset

dataset = load_dataset("plantcad/opengenome2-metagenomes-plantcad2-c4096")

Citation

If you use this dataset, please cite the original OpenGenome2:

@article{Brixi2025.02.18.638918,
    author = {Brixi, Garyk and Durrant, Matthew G and Ku, Jerome and others},
    title = {Genome modeling and design across all domains of life with Evo 2},
    year = {2025},
    doi = {10.1101/2025.02.18.638918},
    journal = {bioRxiv}
}

License

Apache 2.0 (inherited from OpenGenome2)