eggNOG annotation of ORFs
======

eggNOG is a database of gene orthology and functional annotations.

 - Website: http://eggnog5.embl.de/

 - Citation: Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A,
   Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C.
   eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
   orthology resource based on 5090 organisms and 2502 viruses. Nucleic acids
   research. 2019 Jan 8;47(D1):D309-14.

eggNOG release 5.0 was used as the reference for annotation.

 - Source: http://eggnog5.embl.de/download/eggnog_5.0/

eggNOG-mapper v2.1.7 was used to perform annotation. Command:

```
emapper.py --cpu # -i input.faa -o output
```

Statistics:

 - Total number of matches: 119,723,081
 - Number of annotated ORFs: 41,602,267
 - Number of matched seed orthologs: 12,449,486
 - Number of matched OGs (narrowest): 1,794,179
 - Number of matched OGs (all): 2,704,875

Database files:

 - orf-to-seed.map: Mapping of ORFs to seed orthologs. It is a unique mapping.
   The seed orthologs were used to derive other annotation fields such as OGs.

 - seed-to-og.map: Mapping of seed orthologs to Orthologous Groups (OGs). OGs
   are the basic units of the eggNOG database. Only the narrowest (i.e., most
   derived, lowest) OGs in the taxonomic lineage are reported. Note: one seed
   may be mapped to multiple narrowest OGs (although rare).

 - seed-to-og_all.map: Mapping of seed orthologs to OGs of all taxonomic
   ranks.

 - seed-to-category.map: Mapping of seed orthologs to COG categories (single
   letters).

 - seed_description.txt: Description of each seed.

 - seed-to-gene.map: Mapping of seed orthologs to gene names ("Preferred
   name"). It is a unique mapping.

 - og-to-category.map: Mapping of OGs to COG categories. Note: one OG may be
   mapped to multiple categories.

 - og_taxid.txt: NCBI TaxID of each OG. Note: if one OG is mapped to root (1)
   and another TaxID (usually 2 or 2157), the latter is kept.

 - og_description.txt: Description of each OG. Note: Same as above.

 - cog_category.txt: Definition of COG categories.

   - Source: https://www.ncbi.nlm.nih.gov/research/cog/

 - idmaps/: Mapping of seed orthologs to external databases, including:
   
   - GOs, EC, KEGG_ko, KEGG_Pathway, KEGG_Module, KEGG_Reaction, KEGG_rclass,
     BRITE, KEGG_TC, CAZy, BiGG_Reaction, PFAMs

Collapsing order:

```
  ORF > seed > OG > category
         v
      category
```

Raw eggNOG-mapper output files:

 - emapper.hits: DIAMOND hit table (-outfmt 6).

 - emapper.seed_orthologs: Mapping to seed orthologs. Columns:

   - qseqid, sseqid, evalue, bitscore, qstart, qend, sstart, send, pident,
     qcov, scov

 - emapper.annotations: Annotation results. Columns:

   - query, seed_ortholog, evalue, score, eggNOG_OGs, max_annot_lvl, COG_
     category, Description, Preferred_name, GOs, EC, KEGG_ko, KEGG_Pathway,
     KEGG_Module, KEGG_Reaction, KEGG_rclass, BRITE, KEGG_TC, CAZy, BiGG_
     Reaction, PFAMs