🧬 sanger_qc:
A Python script for converting .ab1 files to .fasta and .qual, and trimming sequences based on a moving average of quality scores. sanger_qc is a Python script designed to streamline the process of converting .ab1 files from Sanger sequencing into .fasta and .qual formats, followed by sequence trimming based on quality scores.
🚀 Quick Start:
You can start using sanger_qc with the following commands:
git clone https://github.com/yourusername/sanger_qc.git
cd sanger_qc
pip install -r requirements.txt
#Run the script:
./sanger_qc.py -i /path/to/ab1_files -o /path/to/output_dir -w 10 -q 30.0
⚙️ Installation:
Ensure you have Python 3.6+ installed. Install the required packages with: pip install numpy biopython
🔧 Usage:
Run sanger_qc.py with the following options:
./sanger_qc.py -i <input_directory> -o <output_directory> [-w <window_size>] [-q <quality_cutoff>]
Arguments:
-i, --input_dir: (Required) Directory containing .ab1 files.
-o, --output_dir: (Required) Directory for the output files.
-w, --window_size: (Optional) Window size for moving average (default: 10).
-q, --qual_cutoff: (Optional) Quality score cutoff for trimming (default: 30.0).
📂 Output Structure:
fasta/: Converted .fasta files.
qual/: Converted .qual files.
trimmed_fasta/: Trimmed .fasta files.
trimmed_qual/: Trimmed .qual files.