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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
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