susheelbhanu / kraken2

# Kraken

Kraken2

About

• Repository containing Snakemake workflow for running Kraken2 analyses

Setup

Databases

• Two different Kraken2 databases can be used and can be downloaded from the following sources:

1. kraken2, i.e. maxikraken2_1903_140GB (March 2019, 140GB) :- https://lomanlab.github.io/mockcommunity/mc_databases.html
2. struo2_kraken2 :- http://ftp.tue.mpg.de/ebio/projects/struo2/GTDB_release202/kraken2/

Conda

Conda user guide

# install miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh # follow the instructions

Getting the repository including sub-modules

git clone [e-mail]:susheelbhanu/kraken2.git

Create the main snakemake environment

# create venv
conda env create -f envs/snakemake.yaml -n "snakemake"
conda activate snakemake

How to run

The workflow can be launched using one of the option as follows

./sbatch.sh

(or)

CORES=48 snakemake -s workflow/Snakefile --configfile config/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores $CORES -rpn

(or)

Note: For running on esb-compute-01 or litcrit adjust the CORES as needed to prevent some tools from spawning too many threads; and launch as below

CORES=24 snakemake -s workflow/Snakefile --configfile config/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores $CORES -rpn

Configs

All config files are stored in the folder config/

Note(s):

• Edit the paths to data_dir, results_dir, env_dir and the *databases*
• Provide a kraken2_sample_list