POD5 and FASTQ ID Matching and Filtering - Demultiplexing nanopore pod5 raw files

This repository contains a Python script designed to streamline the process of matching IDs between FASTQ and POD5 files, and creating filtered POD5 files based on these matches.

Features:

• Extracts IDs from FASTQ and POD5 files.
• Matches IDs between FASTQ and POD5 files and generates a matching CSV file.
• Filters and creates new POD5 files containing only the matched IDs.
• Utilizes multi-threading for improved performance.
• Stores temporary CSV files in a dedicated .csv-tmp directory.

Installation:

1. Ensure you have Python 3 installed.
2. Install the pod5 package using pip:

   pip install pod5

   For more details, visit the POD5 package page on PyPI.

Usage:

1. Ensure the pod5 package is installed.
2. Run the script with the appropriate arguments:

   python3 demux_pod5.py --fastq <fastq_directory> --pod5 <pod5_directory> --output_csv <output_csv_file> --output_pod5 <output_pod5_directory> --threads <number_of_threads>

Arguments:

--fastq", "Directory containing FASTQ files

--pod5", "Directory containing original POD5 files

--output_csv", "Output CSV file to save the matching IDs

--output_pod5", "Directory to save new filtered POD5 files

--threads", "Number of threads to use for processing

Requirements:

• Python 3.6+
• pod5 package