Datasets:
File size: 2,490 Bytes
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---
license: apache-2.0
tags:
- bacteria
- biology
- DNA
- clustering
- prokaryotes
pretty_name: Dataset for clustering bacterial genomes (DNA)
size_categories:
- 10K<n<100K
---
# Dataset for whole-bacterial genomes clustering (DNA)
A dataset of 60,710 bacterial genomes across 25 species, 10 genera and 7 families.
The genome DNA sequences have been extracted from [MGnify](https://www.ebi.ac.uk/metagenomics). Each row contains whole bacterial genome, with spaces
separating different contigs present in the genome.
## Labels
The species, genus and family labels have been provided by MGnify
## Usage
We recommend loading the dataset in a streaming mode to prevent memory errors.
```python
from datasets import load_dataset
ds = load_dataset("macwiatrak/bacbench-strain-clustering-dna", split="test", streaming=True)
# fetch the DNA sequence of the genome
item = next(iter(ds))
dna_seq = item["dna_sequence"]
# get DNA sequences for each contig
dna_seq_contigs = dna_seq.split()
```
## Split
The strain clustering task is a fully unsupervised task, therefore, we do not perform any split and the whole dataset is available as part of the `test` split.
See [github repository](https://github.com/macwiatrak/Bacbench) for details on how to embed the dataset with DNA and protein language models as well as code to predict antibiotic
resistance from sequence. For coding sequence representation of the genome see the [strain-clustering-protein-sequences](https://huggingface.co/datasets/macwiatrak/bacbench-strain-clustering-protein-sequences)
dataset.
---
dataset_info:
features:
- name: genome_name
dtype: string
- name: contig_name
sequence: string
- name: dna_sequence
dtype: string
- name: start
sequence:
sequence: string
- name: end
sequence:
sequence: string
- name: locus_tag
sequence:
sequence: string
- name: strand
sequence:
sequence: string
- name: genome_completeness
dtype: string
- name: genome_lineage
dtype: string
- name: genome_sample_accession
dtype: string
- name: genome_study_accession
dtype: string
- name: country
dtype: string
- name: family
dtype: string
- name: genus
dtype: string
- name: species
dtype: string
splits:
- name: test
num_bytes: 169603550566
num_examples: 60710
download_size: 78407309865
dataset_size: 169603550566
configs:
- config_name: default
data_files:
- split: test
path: data/test-*
--- |