README.md

---
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-*
---