krust is a k-mer counter--a bioinformatics 101 tool for counting the frequency of substrings of length k within strings of DNA data. It's written in Rust and run from the command line. It takes a fasta file of DNA sequences and will output all canonical k-mers (the double helix means each k-mer has a reverse complement) and their frequency across all records in the given fasta file.
Run krust on the test data* in the krust Github repo, searching for kmers of length 5, like this:
cargo run --release 5 cerevisae.pan.fa > output.tsvor, searching for kmers of length 21:
cargo run --release 21 cerevisae.pan.fa > output.tsvkrust prints to stdout, writing, on alternate lines:
>{frequency}
{canonical k-mer}
>{frequency}
{canonical k-mer}
...krust uses the rust-bio, rayon, and dashmap Rust libraries.
*Unusual, yes, to provide this data in the repo, but it's helped me spread word about what I'm doing.