A bioinformatics pipeline for manipulating chromosome structures based on AGP and FASTA files, designed for Hi-C scaffolding applications.
This tool performs complex chromosome operations including:
- Extracting chromosome segments from AGP files
- Copying segments between chromosomes
- Inserting segments at specific locations
- Generating modified FASTA files reflecting the new chromosome structures
- Flexible Configuration: Define operations via a simple config file
- Logging: Detailed logging for troubleshooting
- Validation: Input validation and error checking
- Modular Design: Each operation is performed in discrete steps
- Reference Support: Optional reference chromosome integration
- Python 3.6+
- seqkit (for FASTA extraction)
- Standard UNIX tools (awk, grep, cat, etc.)
- Clone this repository:
git clone https://github.com/GengruiZhu/Hmodify.git cd Hmodify