eggnog_download

Tags: eggnog database download annotation functional orthology sample-scope

Download the eggNOG database for functional annotation.

Fetches the pre-computed orthology data and Diamond database required by eggNOG-mapper. This includes the massive protein database and taxonomic information needed for accurate ortholog assignment.

Internet & Storage Required

This process requires an active internet connection and significant disk space (often >50GB) to store the uncompressed database files.

Outputs

record (
    db: Path?,
    db_tarball: Path?,
    logs: Set<Path?>
)

Field	Type	Description
db	Path?	The eggNOG database directory (Diamond database and taxonomy info)
db_tarball	Path?	A compressed tarball of the database (if requested via parameters)
logs	Set<Path?>	Optional program specific log files

Parameters

eggNOG Downloader Parameters

Parameter	Type	Default	Description
--eggnog_db	string		Tarball or path to eggNOG databases
--download_eggnog	boolean	false	Required if downloading latest eggNOG database, will overwrite existing databases.
--eggnog_save_as_tarball	string		Save the eggNOG database as a single tarball
--eggnog_skip_diamond	boolean	false	Do not install the diamond database
--eggnog_install_mmseq	boolean	false	Install the MMseqs2 database
--eggnog_install_pfam	boolean	false	Install the Pfam database, required for de novo annotation or realignment
--eggnog_install_hmm	boolean	false	Install the HMMER database specified with --hmmer_taxid
--eggnog_hmmer_taxid	integer	2	Tax ID of eggNOG HMM database to download

Used By

Subworkflows

• eggnog - Functional annotation through orthology assignment.

Workflows

• eggnog - Functional annotation of proteins using orthologous groups and phylogenies.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• eggNOG-mapper
  Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Mol. Biol. Evol. 34, 2115-2122 (2017)

Source

View source on GitHub

Version

EGGNOG_DOWNLOAD:
    - eggnog-mapper: 2.1.13