Prokaryotic Genome Annotation pipeline

This is a pipeline to run multiple annnotation tools, and compile the output in some nice comparable and easily usable tables. The pipeline is written to work optimally on our own server, and might be challenging to implement other places. However, below are the different steps which should be enough to get things working.

Citation

Installation

miniconda or anaconda is needed

Clone

git clone https://github.com/Russel88/annotation.git

cd annotation

Make conda environment

conda env create -n annotation -f=environment.yml

Install KOfam_scan and download database

See instructions here: ftp://ftp.genome.jp/pub/tools/kofamscan/

wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz

Install eggNOG-mapper and download eggNOG bact diamond database

See instructions here: https://github.com/eggnogdb/eggnog-mapper

Install dbCAN2 and download associated CAZyme databases

git clone https://github.com/Russel88/run_dbcan.git

Download databases as described here https://github.com/linnabrown/run_dbcan

Install SignalP

See instructions here: http://www.cbs.dtu.dk/services/SignalP/

Download and prepare databases

MEROPS

wget ftp://ftp.ebi.ac.uk/pub/databases/merops/current_release/pepunit.lib

awk '{print $1}' pepunit.lib > pepunit.faa

diamond makedb --in pepunit.faa -d merops

TnpPred

Get HMMs:

wget https://www.mobilomics.cl/tnppred/downloads/TnpPred_HMM_Profiles.hmm

hmmpress TnpPred_HMM_Profiles.hmm

RGI

Download database: https://github.com/arpcard/rgi

How to run

Edit the config.yml file to point to the software and databases

conda activate annotation

./annotate -h