Kraken2Polute

This repository contains a Bash script for processing paired-end sequencing data using Kraken2, a taxonomic sequence classifier. The script automates the steps of activating a Conda environment, processing sequencing files, and generating reports.

Prerequisites

• Mamba: A fast alternative to Conda for package management.
• Kraken2: Ensure Kraken2 is installed in your Conda environment.

Installation

1. Install Mamba (if not already installed):

   conda install mamba -n base -c conda-forge

2. Create a Conda environment with Kraken2:

   mamba create -n kraken2 -c bioconda kraken2

3. Activate the environment:

   conda activate kraken2

4. Clone this repository:

   git clone <repository-url>
   cd Kraken2Polute

5. Make the script executable:

   chmod +x kraken2_processing.sh

Usage

Run the script with optional parameters:

./kraken2_processing.sh [options]

Options

• -i, --input-dir: Input directory containing subdirectories with sequencing files (default: Run2_trim)
• -o, --output-dir: Output directory to save results (default: Run4_pollute)
• -d, --db-path: Path to Kraken2 database (default: /home/maolp/data5/All_zhuyue_inluolab/kdb)
• -t, --threads: Number of threads to use (default: 8)
• -e, --conda-env: Conda environment to activate (default: kraken2)
• -h, --help: Display help message

Example

./kraken2_processing.sh -i my_input_dir -o my_output_dir -d /path/to/kraken_db

plots

Then run the script using the command line with the following options:

python Kraken2Polute_plots.py -i <input_directory> -o <output_directory> -t <threshold>

Arguments

• -i, --input_dir: The directory containing .kraken.report files. Default is Run4_pollute.
• -o, --output_dir: The directory where the generated pie chart figures will be saved. Default is Plots.
• -t, --threshold: The percentage threshold for merging small classifications into an "Others" category. Default is 1.0.

Example

python script_name.py -i my_reports -o my_charts -t 0.5