VARCALL (Yersinia Polymorphic Site Caller) v1.5
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healthcareRecord type:
software
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================================================================================ ■ VARCALL (Yersinia Polymorphic Site Caller) v1.5 ■ ================================================================================ 📅 Created: May 15, 2025 👨💻 Author: Oleg Reva (oleg.reva@up.ac.za) Centre for Bioinformatics and Computational Biology, University of Pretoria, South Africa
🔬 Purpose: Automated pipeline for creation of a 0/1 matrix of polymorphic sites from Yersinia genome sequences.
⚙️ Dependencies: ┌───────────────────┬───────────────────────┐ │ Tool │ Minimum Version │ ├───────────────────┼───────────────────────┤ │ Python │ 3.12.3 │ │ BLAST+ │ 2.13.0 │ └───────────────────┴───────────────────────┘
🚀 Usage: python3 varcall.py [project_directory] [options] for example: python3 varcall.py example
🔧 Options: --input_directory Input directory (default: 'input') --output_directory Output directory (default: 'output') --tmp_directory Temp directory (default: 'tmp') --mismatch Allowed mismatch number (default: 6)
📂 Input Requirements: - GenBank files (*.gbk, *.gbf, *.gb) - FASTA files (*.fasta, *.fa, *.fst, *.fas)
📊 Output: - matrix.csv: 0/1 matrix of polymorphic sites - matrix.fa: FASTA format polymorphic sites
🆘 Help Options: -h, --help Show this help -v, --version Show version info ================================================================================