eggNOG-mapper
eggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu-CPU: 2.1.15, via the
bio-appsmodule.
Usage
eggNOG-mapper is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the eggNOG-mapper module:
Databases
eggNOG-mapper requires the eggNOG reference databases. CSC provides a shared copy on
Roihu (eggNOG 5.0.2, with the MMseqs2, Pfam and novel families databases), and the
eggnog-mapper module sets the EGGNOG_DATA_DIR environment variable to it, so
emapper.py finds the databases without further options.
Running eggNOG-mapper
eggNOG-mapper is run with the emapper.py command:
#!/bin/bash
#SBATCH --job-name=emapper
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G
module load bio-apps/v202603
module load eggnog-mapper/2.1.15
emapper.py --cpu $SLURM_CPUS_PER_TASK \
-i proteins.fasta -o annotation
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.