This pipeline is based on USEARCH that is a propetary software. Please, read the software policy before using it.
This short pipeline is supposed to run on HPCC mounting the SLURM system.
You will need to:
- clone the repo
git clone [email protected]:Gian77/Demultiplex-USEARCH.git
; - put all your files in the
rawdata
directory, including the barcode files. - modify the
config.yml
file adding the full PATHs to your files; - run the pipeline
sbatch demultiplex-usearch.sb
.
All generated files will be in the output_dir/
.
NOTE
- If you have a very large datasets, to increased the alllocated time, RAM, and CPU requirements you should modify the
demultiplex-usearch.sb
script.
#SBATCH --time=00:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G