Replaces manual FASTA parsing and subprocess calls with efficient random access indexing. Implements a pure-Python interface for extracting genomic subsequences without loading entire files into memory.
Tech Stack
PythonBiology & Biotechnology
Why pyfaidx?
• Pure Python implementation
• Thread-safe file access
• Automatic index creation
Limitations
• Slower than C-based samtools for bulk tasks
• Limited to FASTA format
• Index files are not cross-compatible with all tools
1/30/2026
Last Update
76
Forks
3
Issues
Other
License
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