eggnog
Tags: functional annotation orthology eggnog protein-domains sample-scope
Functional annotation through orthology assignment.
This subworkflow performs genome-wide functional annotation using eggNOG-mapper, which provides fast functional annotation through orthology assignment. It can optionally download the eggNOG database if not provided. The pipeline predicts orthologs, functional categories, and various annotation formats including GFF, Excel, and detailed reports.
Take
proteins: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
proteins | Protein sequences in FASTA format for functional annotation |
database: Path?
download_eggnog: Boolean
save_as_tarball: Boolean
| Name | Type | Description |
|---|---|---|
database | Path? | Path to pre-downloaded eggNOG database (optional) |
download_eggnog | Boolean | Boolean flag to trigger database download if not provided |
save_as_tarball | Boolean | Boolean flag to save downloaded database as tarball |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
hits | Raw search hits (Diamond/MMseqs2) against the eggNOG database |
seed_orthologs | List of identified seed orthologs used for annotation transfer |
annotations | Main tab-delimited annotation file (COGs, KEGG, GO, etc.) |
xlsx | Excel format of the annotations file |
orthologs | List of fine-grained orthologs (optional) |
genepred | Predicted gene sequences (optional) |
gff | Annotations in GFF format (optional) |
no_anno | FASTA file of sequences that failed to be annotated (optional) |
pfam | Raw PFAM domain hits (optional) |
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- eggnog_download - Download the eggNOG database for functional annotation.
- eggnog_mapper - Functional annotation of proteins using eggNOG orthology data.
Used By
This subworkflow is used by the following 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)