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README.md
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---
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license: apache-2.0
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---
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## Overview
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This dataset consists of reference genomes for 10 species:
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| Species | Assembly Accession |
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|--------------------------|-----------------------------------------------------|
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| *Arabidopsis thaliana* | `GCF_000001735.4_TAIR10.1` |
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| *Caenorhabditis elegans* | `GCF_000002985.6_WBcel235` |
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| *Danio rerio* | `GCF_000002035.6_GRCz11` |
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| *Drosophila melanogaster*| `GCF_000001215.4_Release_6_plus_ISO1_MT` |
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| *Felis catus* | `GCF_018350175.1_F.catus_Fca126_mat1.0` |
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| *Gallus gallus* | `GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b` |
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| *Gorilla gorilla* | `GCF_029281585.2_NHGRI_mGorGor1-v2.0_pri` |
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| *Homo sapiens* | `GCF_000001405.40_GRCh38.p14` |
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| *Mus musculus* | `GCF_000001635.27_GRCm39` |
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| *Salmo trutta* | `GCF_901001165.1_fSalTru1.1` |
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Each item in the dataset contains the following fields:
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```
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"sequence": datasets.Value("string"),
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"species_label": datasets.ClassLabel() # See below
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"description": datasets.Value("string"),
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"start_pos": datasets.Value("int32"),
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"end_pos": datasets.Value("int32"),
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"fasta_url": datasets.Value("string")
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```
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The class labels are as follows:
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| Class | Label |
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|-----------------------------|-------|
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| `'Homo_sapiens'` | 0 |
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| `'Mus_musculus'` | 1 |
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| `'Drosophila_melanogaster'` | 2 |
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| `'Danio_rerio'` | 3 |
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| `'Caenorhabditis_elegans'` | 4 |
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| `'Gallus_gallus'` | 5 |
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| `'Gorilla_gorilla'` | 6 |
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| `'Felis_catus'` | 7 |
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| `'Salmo_trutta'` | 8 |
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| `'Arabidopsis_thaliana'` | 9 |
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## Usage
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To use this dataset, set the `chunk_length` (length of each sequence, in base-pairs) and the `overlap` (amount each sequence overlaps, in base-pairs).
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The dataset only contains a `train` split.
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We recommend randomly splitting the dataset to create validation/test sets.
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See below for example usage:
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```python
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import datasets
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max_length = 32_768
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overlap = 0
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dataset = datasets.load_dataset(
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'yairschiff/ten_species',
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split='train', # original dataset only has `train` split
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chunk_length=max_length,
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overlap=overlap,
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trust_remote_code=True
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)
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self.dataset = dataset.train_test_split(
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test_size=0.05, seed=42)[split]
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```
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## Acknowledgments
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Code for dataset processing is derived from https://huggingface.co/datasets/InstaDeepAI/multi_species_genomes.
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