Representative Genomes

- HRGMv2_Rep_Genome/
    : Genome sequences (FASTA format) for 4,824 HRGMv2 representative genomes (one per species)
- HRGMv2_Rep_Genome.tar.gz
    : Compressed archive of the HRGMv2_Rep_Genome/ folder

Pangenomes

- HRGMv2_Pangenomes/

    : Pangenome data for all 4,824 species, structured as follows:

    For Multi-genome species (2,639 species): Species with more than one non-redundant genome. Each folder contains the full output of Panaroo v1.3.0. 
    (Refer to the Panaroo GitHub for detailed file descriptions.)

        - combined_DNA_CDS.fasta.gz
        - combined_protein_CDS.fasta.gz
        - combined_protein_cdhit_out.txt
        - combined_protein_cdhit_out.txt.clstr
        - final_graph.gml
        - gene_data.csv.gz
        - gene_presence_absence.csv
        - gene_presence_absence.Rtab
        - gene_presence_absence_roary.csv
        - pan_genome_reference.fa – nucleotide sequences
        - pan_genome_reference.faa – amino acid sequences
        - pre_filt_graph.gml
        - struct_presence_absence.Rtab
        - summary_statistics.txt
        - emapper_results/ – eggNOG-mapper results for pan_genome_reference.fa
        - rgi_results/ - RGI results for pan_genome_reference.fa

    For Single-genome species (2,185 species): Species with only one non-redundant genome. Pangenomes were generated directly from the representative genome, including:

        - pan_genome_reference.fa – nucleotide sequences
        - pan_genome_reference.faa – amino acid sequences
        - emapper_results/ – eggNOG-mapper results for pan_genome_reference.fa
        - rgi_results/ – RGI results results for pan_genome_reference.fa

- For bulk download:

    1. HRGMv2_Pangenomes.tar.gz – Archive of the entire HRGMv2_Pangenomes/ folder
    2. Pangenome_download_link_info.tsv – Table with full download URLs for each species