README for eccToolkit

Welcome to the eccToolkit repository. This repository contains the analytical code employed in the research paper titled "Dynamics of Extrachromosomal Circular DNA in Rice."

Overview

eccToolkit is a specialized software suite designed for the analysis and classification of eccDNA (extrachromosomal circular DNA) elements. It comprises two main scripts: eccDNA_Repeat_Classifier.py and eccDNA_Detected_eccDNA.py, which together facilitate the detection and categorization of eccDNA sequences from genomic data.

Features

• eccDNA Detection: Identifies eccDNA elements within genomic data.
• Repeat Classification: Classifies detected eccDNA elements based on their repeat characteristics.
• Comprehensive Analysis: Integrates various data processing steps to provide detailed insights into eccDNA profiles.

Requirements

• Python environment with necessary dependencies installed (e.g., Pandas, NumPy).
• Genomic data files in appropriate formats (e.g., BED, FASTA).

Installation

Using Mamba (Recommended)

1. Install Mamba via Miniconda or Anaconda, if not already installed.

2. Create and activate the eccToolkit environment:

   mamba env create -f eccToolkit.yml
   conda activate eccToolkit

Using Conda

1. Alternatively, use Conda for installation:

   conda env create -f eccToolkit.yml
   conda activate eccToolkit

Script Usage and Parameters

eccDNA_Detected_eccDNA.py

This script is responsible for the initial detection of eccDNA elements from genomic data.

Parameters:

• -i, --input (Required): Path to the input genomic data file.
• -o, --output (Required): Path for the output file where detected eccDNA elements will be listed.
• Additional parameters specific to the detection algorithm (e.g., sensitivity settings).

Example Usage:

python eccDNA_Detected_eccDNA.py -i input_genomic_data.bed -o detected_eccDNA.csv

Input/Output:

• Input: BED format genomic data.
• Output: CSV file listing detected eccDNA elements.

eccDNA_Repeat_Classifier.py

This script classifies the detected eccDNA elements based on their repeat characteristics.

Parameters:

• -i, --input (Required): Path to the input file containing detected eccDNA elements.
• -o, --output (Required): Path for the output file where classified eccDNA elements will be listed.
• Additional parameters for classification criteria (e.g., repeat length, type).

Example Usage:

python eccDNA_Repeat_Classifier.py -i detected_eccDNA.csv -o classified_eccDNA.csv

Input/Output:

• Input: CSV file from eccDNA_Detected_eccDNA.py.
• Output: CSV file with eccDNA elements classified by repeat type.

Comprehensive Workflow

To fully utilize eccToolkit, follow these steps:

1. Run eccDNA_Detected_eccDNA.py to detect eccDNA elements.
2. Use the output of the first script as the input for eccDNA_Repeat_Classifier.py to classify the detected elements.

License

This project is licensed under the GNU General Public License v3.0. Kindly refer to the LICENSE file for detailed terms and conditions.