16S_DADA2

About

• This repository can be used for the analyses of 16S sequencing data via DADA2 using a snakemake workflow

Set up

git clone https://github.com/susheelbhanu/16S_DADA2.git

• You might want to adjust some settings in the files config/sbatch.sh and config/config.yaml, e.g. the name of the snakemake conda environment, paths and number of cores/threads.

Setting up samples.tsv and metadata.tsv

Step1:

• There is no other option but to create a metadata file outside of this workflow and import
• NOTE: the first column of the metadata file should be named, "Sample"
• Import file and place in the config folder

Step2:

• Edit line 15, i.e. path to the fastq.gz files in the notes/samples_tsv.sh script
• From the 16S_DADA2 folder run the following:

bash notes/samples_tsv.sh

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
# create venv
conda env create -f requirements.yml -n "YourEnvName"

Run the analysis

# in an interactive session
./config/sbatch.sh
# as a slurm job
sbatch ./config/sbatch.sh