Methylotl is a Python package designed to process raw bisulfite sequencing data. It performs essential steps to convert, align, and analyze bisulfite-treated DNA sequences, providing insights into DNA methylation patterns.
- Aligns bisulfite-treated reads to a reference genome
- Analyzes methylation patterns
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Python 3.10 or higher
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Required Python packages:
pysam -
External tools:
fastqc,trimgalore,bsmapz,samtools,methyldackel
Note: This tool has been tested and is confirmed to work correctly on Debian-like distributions.
- Clone the repository:
git clone https://github.com/yourusername/Methylotl.git
cd Methylotl
- Run the install.sh script to create a conda environment and install the necessary tools:
chmod +x install.sh
./install.sh
To index the genome, run the following command:
python Methylotl.py index --genome /path/to/genome.fa
To process reads with default settings, use the following command:
python Methylotl.py process --input_dir /path/to/input --output_dir /path/to/output --ref /path/to/genome.fa --logs /path/to/logs --q 20
index: Index the genome.
--genome: Path to the reference genome file.
process: Process reads.
--threads: Number of threads to use (default: 8).--input_dir: Absolute path to the input folder.--output_dir: Absolute path to the output folder.--ref: Absolute path to the genome file.--logs: Absolute path to the logs folder.--q: Quality score for trim_galore (default: 20).
Methylotl generates the following output files:
- FastQC reports: Before and after trimming
- Trimmed FASTQ files
- Unsorted BAM files
- Sorted BAM files
- Deduplicated BAM files
- BedGraph report
- Methylation bias (MBias) plot for each strand (in SVG format)
- Log files for each step of the process
Contributions are welcome! Please fork the repository and submit pull requests with detailed descriptions of your changes.
This project is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. See the LICENSE file for more details.
For questions or comments, please contact us [email protected] , [email protected].