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

If you have not installed Rust yet, please visit rustup.rs to install it.

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::{complement_char, 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]);

Benchmarks

simd-minimizers-bench/benches/bench.rs contains benchmarks used in this blogpost.

simd-minimizers-bench/src/bin/paper.rs contains benchmarks used in the paper.

Note that the benchmarks require some nightly features, you can install the latest nightly version with

rustup install nightly

To replicate results from the paper, go into simd-minimizers-bench and run

RUSTFLAGS="-C target-cpu=native" cargo +nightly run --release
python eval.py