Directory Structure

The DIGS-for-EVEs repository is organized to categorize EVE loci based on host species groups, virus subdivisions, and catalog version, as follows:

DIGS-for-EVEs/
└── eve/
    └── animals/
        └── vertebrates/
            └── nonretroviral/
                └── version-1.0/
                    ├── input/
                    └── output/

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Subdirectories

• eve/
  Contains versioned catalogs of EVE loci.

  • animals/
    Subdivision based on host species group.

    • vertebrates/
      Further subdivision of the host group.

      • nonretroviral/
        Subdivision by virus group, non-retroviral viruses in this case.

        • version-1.0/
          Version of the catalog for this host & virus subdivision.

          • input/
            Contains files used as input for genome screening.

          • output/
            Contains the results and summary of the genome screen.

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Detailed Contents

input/ Directory

• Virus polypeptide probe sequences used for screening (FASTA format).
• Reference protein sequence library used for classifying hits recovered by screening (FASTA format).
• Details of the WGS assemblies screened in this project (assembly files are not included due to their large sizes).
• Control file used with the DIGS tool to implement systematic in silico genome screening.

output/ Directory

• Tables exported from screening databases (includes digs_results table with nucleotide sequences of EVE loci).
• Summary statistics desribing screening results.
• A catalog of endogenous viral element loci identified within this host group.

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