Rust reimplementation of kallisto hits 2.7× speedup with exact parity, author nods
lpachter · x · 2026-10-20
- kallistors is a Rust-native reimplementation of kallisto-style pseudoalignment and RNA-seq quantification, claiming a 2.7× speedup with exact parity on real data (MIT license).
- It loads kallisto v13-compatible indexes, quantifies paired/single-end reads with kallisto-style outputs (abundance.tsv, runinfo.json, abundance.h5), and supports single-cell BUS workflows including BAM I/O.
- kallisto's original author Lior Pachter welcomed the port but noted validation and feature coverage (bustools, lr-kallisto, kb-python, etc.) still have a way to go.
- v0.5.0 brings the latest speedups; the repo is early-stage with 6 stars.
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