simd-minimizers

A SIMD-accelerated library to compute random minimizers.

It can compute all the minimizers of a human genome in 4 seconds using a single thread. It also provides a canonical version that ensures that a sequence and its reverse-complement always select the same positions, which takes 6 seconds on a human genome.

The underlying algorithm is described in the following preprint:

• SimdMinimizers: Computing random minimizers, fast. Ragnar Groot Koerkamp, Igor Martayan bioRxiv 2025.01.27 doi.org/10.1101/2025.01.27.634998

Requirements

This library supports AVX2 and NEON instruction sets. Make sure to set RUSTFLAGS="-C target-cpu=native" when compiling to use the instruction sets available on your architecture.

RUSTFLAGS="-C target-cpu=native" cargo run --release

Usage example

Full documentation can be found on docs.rs.

// Packed SIMD version.
use packed_seq::{PackedSeqVec, SeqVec};
let seq = b"ACGTGCTCAGAGACTCAG";
let k = 5;
let w = 7;

let packed_seq = PackedSeqVec::from_ascii(seq);
let mut minimizer_positions = Vec::new();
simd_minimizers::canonical_minimizer_positions(packed_seq.as_slice(), k, w, &mut minimizer_positions);
assert_eq!(minimizer_positions, vec![3, 5, 12]);