pyBioinfo

A Python toolkit for bioinformatics analysis workflows.

Features

• RNA-Seq analysis pipeline
• ChIP-Seq processing tools
• Genome annotation utilities
• Sequence manipulation tools
• Wrappers for popular bioinformatics tools:
  • Bowtie2
  • featureCounts
  • antiSMASH
  • BigScape
  • MASH

Installation

# Clone the repository
git clone https://github.com/snail123815/pybioinfo.git
cd pybioinfo

# Install dependencies
pip install -r requirements.txt

Usage Examples

RNA-Seq Analysis

python rnaSeq_raw_to_counts.py --raw path/to/reads/*.fastq.gz --out results/ --gbk genome.gbk --isPe --ncpu 4

See RNA-Seq documentation for more details.

antiSMASH Analysis

python run_antismash.py path/to/genomes/*.gbk --completeness 2 --threads 4

Module Coverage

Module	Coverage
bio_sequences
wrappers
basic

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.