eggnog_mapper

Tags: functional-annotation orthology cog kegg go proteins eggnog sample-scope

Functional annotation of proteins using eggNOG orthology data.

Uses eggNOG-mapper to assign functional annotations to protein sequences. It uses precomputed orthologous groups (OGs) to infer functions like COG categories, KEGG pathways, GO terms, and CAZymes with high precision.

Database Required

Requires the eggNOG database (including the diamond database and taxonomic data) to be available.

Inputs

record (
    meta: Record,
    faa: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
faa	Path	Protein sequences in FASTA format (amino acids)

db: Path

Name	Type	Description
db	Path	Directory or compressed tarball containing the eggNOG database

Outputs

record (
    meta: Record,
    hits: Path,
    seed_orthologs: Path,
    annotations: Path,
    xlsx: Path?,
    orthologs: Path?,
    genepred: Path?,
    gff: Path?,
    no_anno: Path?,
    pfam: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
hits	Path	Raw search hits (Diamond/MMseqs2) against the eggNOG database
seed_orthologs	Path	List of identified seed orthologs used for annotation transfer
annotations	Path	Main tab-delimited annotation file (COGs, KEGG, GO, etc.)
xlsx	Path?	Excel format of the annotations file
orthologs	Path?	List of fine-grained orthologs
genepred	Path?	Predicted gene sequences
gff	Path?	Annotations in GFF format
no_anno	Path?	FASTA file of sequences that failed to be annotated
pfam	Path?	Raw PFAM domain hits
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

eggNOG Mapper Parameters

Parameter	Type	Default	Description
--eggnog_genepred	string	search	Method to use for gene prediction (choices: search, prodigal)
--eggnog_mode	string	diamond	Method to search against eggNOG sequences (choices: diamond, hmmer, mmseqs, cache, no_search)

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)

• DIAMOND
  Buchfink B, Xie C, Huson DH Fast and sensitive protein alignment using DIAMOND. Nat. Methods. 12, 59-60 (2015)

Source

View source on GitHub

Version

EGGNOG_MAPPER:
    - eggnog-mapper: 2.1.13