Metabinner

Requirements

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 https://github.com/dixit-kunal/Metabinner.git
cd Metabinner

Create the main snakemake environment

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

Setup

• Place your preprocessed/trim reads (e.g. sample_R1.fastq.gz and sample_R2.fastq.gz files) in a reads folder
• Place the individual assemblies (e.g. sample.fasta) into an assembly folder
• Modify the config/config.yaml file to change the different paths and eventually the different options
• Modify the config/sample_list.txt file to include your samples

Without Slurm

snakemake -rp --cores 28 --use-conda

With Slurm

• Modify the config/slurm.yaml file by checking partition, qos and account that heavily depends on your system
• Modify the config/sbatch.sh file by checking #SBATCH -p, #SBATCH --qos= and #SBATCH -A options that heavily depends on your system

sbatch config/sbatch.sh

Folder structure

• Snakefiles: snakemake-based scripts for launching Metabinner, MAG taxonomy and quality analyses and integron coordinate retrieval
• config: folder containing all config files required for Snakefiles
• workflow: folder containing rules and snakefile
• envs: folder containing all conda environments
• scripts: folder containing supplementary scripts