Nanopore Demultiplex with Bowtie

Using a meta_data.tsv file describing 5' and 3' barcodes the tool de-multiplexes reads from fastq files (Guppy basecalling output) into individual folders.

Usage

Setup

# install dependencies
pip install -r requirements.txt
sudo apt-get install -y bowtie

Run

#input directory: pass folder from guppy_basecaller
python3 main.py --input_directory {path/to/input/directory/} 
                --output_directory {path/to/output/directory} 
                --threads {threads_for_multiprocessing}

Details

An example file for meta_data.tsv is available. The file should be edited and placed in the folder 'pass' created by guppy_basecaller. Columns G to J are required.