eggnog

Tags: functional-annotation orthology proteins eggnog bactopia-tool

Functional annotation of proteins using orthologous groups and phylogenies.

This Bactopia Tool uses eggNOG-mapper to assign functional annotation to protein sequences. eggNOG-mapper uses orthologous groups and phylogenies from the eggNOG database to more precisely functionally annotate than traditional homology methods.

Usage

Bactopia CLI:

bactopia --wf eggnog \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/eggnog/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── eggnog-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.emapper.annotations
│           ├── <SAMPLE_NAME>.emapper.hits
│           ├── <SAMPLE_NAME>.emapper.seed_orthologs
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── eggnog-<TIMESTAMP>
        └── nf-reports
            ├── eggnog-dag.dot
            ├── eggnog-report.html
            └── eggnog-timeline.html

Annotation

File	Description
*.emapper.annotations	Results from the annotation phase
*.emapper.hits	Results from the search phase (HMMER, Diamond or MMseqs2)
*.emapper.seed_orthologs	Results from parsing the hits
*.emapper.annotations.xlsx	Annotations in Excel format
*.emapper.orthologs	List of orthologs found for each query
*.emapper.genepred.fasta	Sequences of predicted CDS
*.emapper.gff	GFF of predicted CDS
*.emapper.no_annotations.fasta	Sequences without annotation
*.emapper.pfam	Positions of PFAM domains identified

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
eggnog-dag.dot	The Nextflow DAG visualization
eggnog-report.html	The Nextflow Execution Report
eggnog-timeline.html	The Nextflow Timeline Report
eggnog-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Type	Default	Description
--bactopia	string		The path to bactopia results to use as inputs

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

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)

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Type	Default	Description
--include	string		A text file containing sample names (one per line) to include from the analysis
--exclude	string		A text file containing sample names (one per line) to exclude from the analysis

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• eggnog - Functional annotation through orthology assignment.

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)

• eggNOG 5.0 Database
  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, Bork P eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309-D314 (2019)

Source

View source on GitHub