dbCAN_meta_server

This repo contains code obtained from http://bcb.unl.edu/dbCAN2/download/

SignalP is not included here. See https://services.healthtech.dtu.dk/service.php?SignalP-6.0.

Setup

dbCAN meta server analyses need several dependencies in order to run, including:

• Diamond
• HMMER
• natsort
• fraggenescan One way to get all of the dependencies is to create and then activate new conda environment.

conda create -n dbcan -c bioconda diamond hmmer prodigal natsort fraggenescan perl-bioperl
conda activate dbcan

Alternatively, if you plan on using this program with anvi'o, you can just activate that environment (we'll assume it's called anvio5) and then install packages required for dbcan inside there. For example:

conda activate anvio5
conda install natsort fraggenescan

Next, you'll need to clone this dbCAN_meta_server repo locally, and navigate to the db directory inside.

git clone https://github.com/SonnenburgLab/dbCAN_meta_server.git
cd dbCAN_meta_server/db

With your chosen conda environment still active, and within the dbCAN_meta_server/db folder, run:

bash get_and_configure_db_files.sh

Everything is now ready to go!

Running dbCAN_meta_server

To run this program, you can either add /path/to/dbCAN_meta_server to your $PATH, or just point to run_dbcan.py.

python /path/to/dbCAN_meta_server/run_dbcan.py

Running run_dbcan.py with no options (or with -h) will give you the usage instructions.

To run all analyses on a single prokaryote (prok) genome, just do:

python /path/to/run_dbcan.py --cluster --out_dir dbcan_output genome.fasta prok

To run all analyses on protein sequences, just do:

python /path/to/run_dbcan.py --cluster --gff gene_calls.gff --out_dir dbcan_output proteins.faa protein

Full pipeline from anvio:

Anvio command:

anvi-export-gene-calls -c CONTIGS.db -o gene_calls.txt
anvi-get-sequences-for-gene-calls -c CONTIGS.db --get-aa-sequences -o proteins.faa

dbCAN_meta_server commands:

python /path/to/anvi-script-convert-genecalls-to-gff.py gene_calls.txt
python /path/to/run_dbcan.py --cluster --gff gene_calls.txt.gff --out_dir dbcan_output proteins.faa protein
python /path/to/anvi-script-convert-dbCAN-to-functions.py dbcan_output (--export_all)

Anvio command:

anvi-import-functions -c CONTIGS.db -i dbcan_functions_default.txt (or dbcan_functions_all.txt)

You did it!