kmerust

A fast, parallel k-mer counter for DNA sequences in FASTA files.

Features

• Fast parallel processing using rayon and dashmap
• Canonical k-mers - outputs the lexicographically smaller of each k-mer and its reverse complement
• Flexible k-mer lengths from 1 to 32
• Handles N bases by skipping invalid k-mers
• Jellyfish-compatible output format for easy integration with existing pipelines
• Tested for accuracy against Jellyfish

Installation

From crates.io

cargo install kmerust

From source

git clone https://github.com/suchapalaver/kmerust.git
cd kmerust
cargo install --path .

Usage

kmerust <k> <path>

Arguments

• <k> - K-mer length (1-32)
• <path> - Path to a FASTA file

Options

• -h, --help - Print help information
• -V, --version - Print version information

Examples

Count 21-mers in a FASTA file:

kmerust 21 sequences.fa > kmers.txt

Count 5-mers:

kmerust 5 sequences.fa > kmers.txt

FASTA Readers

kmerust supports two FASTA readers via feature flags:

• rust-bio (default) - Uses the rust-bio library
• needletail - Uses the needletail library

To use needletail instead:

cargo run --release --no-default-features --features needletail -- 21 sequences.fa

Output Format

Output is written to stdout in FASTA-like format:

>{count}
{canonical_kmer}

Example output:

>114928
ATGCC
>289495
AATCA

Library Usage

kmerust can also be used as a library:

use kmerust::run::run;
use std::path::PathBuf;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let path = PathBuf::from("sequences.fa");
    run(path, 21)?;
    Ok(())
}

Performance

kmerust uses parallel processing to efficiently count k-mers:

• Sequences are processed in parallel using rayon
• A concurrent hash map (dashmap) allows lock-free updates
• FxHash provides fast hashing for 64-bit packed k-mers

License

MIT License - see LICENSE for details.