Phages & DuckDB: The mighty duo against the giants
summary
Sinfage is an open-source pipeline that uses DuckDB to parse messy semi-structured genomic files, infer schemas, extract metadata and replace Python loops with SQL joins and column expressions. It produces GC-content and synteny diagrams, implements a blast top-hit macro and wildcard-driven file ingestion, turning error-prone, multi-hour pipelines into interactive minutes on a laptop or HPC. The tool is portable as a single binary and already handles large phage collections for safe annotation and visualization.
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chapters (8)
- 0:00Phage therapy introduction
- 1:05Phage research challenges
- 2:50Sim Phage software project
- 4:15DuckDB in bioinformatics
- 6:43DuckDB features for analysis
- 8:10Portability with DuckDB
- 9:37Collinearity analysis benefits
- 10:00Conclusion
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