Dataset Card for AllTheBacteria-FCGR-6mer

This dataset contains the Frequency matrix of the Chaos Game Representation of DNA (FCGR) using 6-mers for the AllTheBacteria dataset paper

The set of assemblies used to create the FCGRs can be found here https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/

Dataset Details

The dataset is ordered the same way the assemblies are provided, each .tar.gz file contains a collection of FCGR, one for each assembly.

FCGRs can be visualized, and saved as images using https://github.com/AlgoLab/complexCGR

Dataset Sources

The dataset was used in panspace

• Repository: https://github.com/pg-space/panspace
• Paper: PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases

Uses

Classification of assemblies based on the FCGR representation

Dataset Structure

The dataset is ordered the same way the assemblies are provided, each .tar.gz file contains a collection of FCGR, one for each assembly.

Dataset Creation

Dataset was created using a snakemake pipeline

See https://github.com/pg-space/panspace/blob/master/scripts/fcgr_allthebacteria.smk

Source Data

The set of assemblies used to create each FCGR can be found in the EBI repository https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/

Who are the source data producers?

Assemblies were produced by the authors of AllTheBacteria dataset, see publication

FCGRs were created by Jorge Avila, Luca Denti and Simone Ciccolella

links of interest

https://github.com/pg-space/fcgr https://github.com/pg-space/panspace

Citation

BibTeX:

@article{cartes2025panspace,
  title={PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases},
  author={Cartes, Jorge Avila and Ciccolella, Simone and Denti, Luca and Dandinasivara, Raghuram and Vedova, Gianluca Della and Bonizzoni, Paola and Sch{\"o}nhuth, Alexander},
  journal={bioRxiv},
  pages={2025--03},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

APA:

Cartes, J. A., Ciccolella, S., Denti, L., Dandinasivara, R., Vedova, G. D., Bonizzoni, P., & Schönhuth, A. (2025). PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases. bioRxiv, 2025-03.

Glossary [optional]

FCGR: Frequency matrix of the Chaos Game Representation of DNA