PANORAMA Testing Dataset

Overview

This repository contains datasets used by our developed tool in GitHub workflows. The datasets are essential for testing, validation, and demonstration purposes within our continuous integration and deployment pipelines.

Dataset

Description

The dataset is composed of Vibrio species presenting more than 50 complete genomes in NCBI databases: RefSeq and Genbank, at the date of 26.06.2025.

Taxid	species	#complete genomes
666	Vibrio_cholerae	614
670	Vibrio_parahaemolyticus	280
663	Vibrio_alginolyticus	107
669	Vibrio_harveyi	69
47951	Vibrio_cyclitrophicus	64
672	Vibrio_vulnificus	63
680	Vibrio_campbellii	51

Files list

Dataset	Description	Usage

Reproduce the Dataset

First, we download the genomes based on the assembly summary with genome_updater

# You must install genome_updater first

Update the dataset

The update of the dataset must be done with precaution, because it will change the expected results.

Update the genomes

# You should install genome_updater before
# 662 is the Vibrio Genus Taxid
mkdir -p Genomes/Vibrio
cd Genomes
# Download the genomes
genome_updater.sh -T 662 -M ncbi -o Vibrio -f 'assembly_report.txt' -l 'complete genome' -d 'refseq,genbank' -t 10
# Search the species with more than 50 genomes
cut -d$'\t' -f7,8 Vibrio/assembly_summary.txt | sed s"/Vibrio /Vibrio\_/"| sed 's/sp. /sp./' | sed -e "s/\(^[0-9]*\tVibrio\_[a-zA-Z0-9_.]*\) .*/\1/" | awk -v min_genomes=50 -F '\t' ' {c[$0]++} END{for (i in c) if (c[i]>=min_genomes) printf("%s\t%s\n",i,c[i])}' | sort -k3 -rn > select_species
# Download the genomes for each species
while read taxid sp nb_genomes;
do 
  mkdir $sp
  genome_updater.sh -T $taxid -M ncbi -o $sp -f 'genomic.gbff.gz' -l 'complete genome' -d 'refseq,genbank' -t 10
  [ $(ls -1 $sp/*/files/ | wc -l) -ne $nb_genomes ] && echo "The number of download genomes is incorrect."
done < select_species.tsv

#Update the pangenomes by following the next part

Update the pangenomes

If you update the genomes before, follow the command below, else you can go to the next command.

License

This repository is licensed under the CECILL License. By contributing to this repository, you agree to license your contributions under the same license.

Contact

For questions or suggestions regarding this dataset repository, please open an issue or contact the repository maintainers.