A Fake Shell for Pangenomics

a month ago

FlatGFA is an efficient pangenomics toolkit with a zero-copy data format, making it identical in memory and on disk, which allows skipping serialization/deserialization and using mmap for fast file opening.
To promote adoption among genomicists, the author explored CLI and Rust API options but found them limited; instead, they built Flash, a fake shell that uses shell syntax to run workflows while internally optimizing with a vectorized interpreter and avoiding I/O overhead.
Flash translates shell scripts into an instruction-based IR, special-cases pangenomic tools to call Rust functions directly, supports mixed resource types (e.g., in-memory stores and files), and implements optimizations like deduplication and format switching for speedups up to 28× compared to traditional shells.

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