A Snakemake workflow to create a dereplicated KEGG database

A simple workflow that creates a dereplicated KEGG GENES database by KO. The workflow needs a KEGG GENES, only available by subscription at the moment.

The workflow performs the following steps:

Map the KEGG GENES to KEGG Orthology (KO) and create a global MMseqs2 database for the KEGG GENES.
Create a MMseqs2 subdatabase for each KO containing the KEGG GENES.
Dereplicate the KEGG GENES for each KO using the cluster module of MMseqs2.
Get representative sequences for each KO using the result2repseq module of MMseqs2 and create a fastA file for each KO.
Combine all fastA files into a single fastA file.

One can run the workflow using the following command:

snakemake --snakefile /vol/cloud/geogenetics/repos/kegg-db-setup/Snakefile -d ./ \
    --configfile config/config.yaml --use-conda -j 100 \
    --conda-frontend mamba --latency-wait 60 \
    --cluster-config config/cluster.yaml \
    --cluster "sbatch --export=ALL -t {cluster.time} --ntasks-per-node {cluster.ntasks_per_node} --nodes {cluster.nodes} --cpus-per-task {cluster.cpus_per_task} --partition {cluster.partition} --job-name {rulename}.{jobid} --output=$(pwd)/slurm-%j.out"

Example using SLURM as a job scheduler.

In the config file, one would be interested in modifying the following parameters:

# Clustering parameters
mmseqs_cluster_min_seq_id: 0.9
mmseqs_cluster_coverage: 0.8
mmseqs_cluster_coverage_mode: 0
mmseqs_cluster_mode: 2

genomewalker/kegg-db-setup

A Snakemake workflow to create a dereplicated KEGG database