diff --git a/README.md b/README.md index f86b6e8..37878ab 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,19 @@ -`krust` is a [k-mer](https://en.wikipedia.org/wiki/K-mer) counter written in Rust and run from the command line that will output canonical k-mers and their frequency across the records in a fasta file. +`krust` is a [k-mer](https://en.wikipedia.org/wiki/K-mer) counter written in Rust and run from the command line that will output canonical k-mers and their frequency across the records in a fasta file. + +Run `krust` on the test data in the [`krust` Github repo](https://github.com/suchapalaver/krust), searching for kmers of length 5, like this: +```$ cargo run --release 5 cerevisae.pan.fa > output.tsv``` +or, searching for kmers of length 21: +```$ cargo run --release 21 cerevisae.pan.fa > output.tsv``` `krust` prints to `stdout`, writing, on alternate lines: ```>{frequency}``` ```{canonical k-mer}``` +```>{frequency} +```>(canonical k-mer}``` +... `krust` uses [`rust-bio`](https://docs.rs/bio/0.38.0/bio/), [`rayon`](https://docs.rs/rayon/1.5.1/rayon/), and [`dashmap`](https://docs.rs/crate/dashmap/4.0.2). -Run `krust` on the test data in the [`krust` Github repo](https://github.com/suchapalaver/krust), searching for kmers of length 5, like this: -```$ cargo run --release 5 cerevisae.pan.fa > output.tsv``` -or, searching for kmers of length 21: -```$ cargo run --release 21 cerevisae.pan.fa > output.tsv``` - Future: A function like fn single_sequence_canonical_kmers(filepath: String, k: usize) {} Would returns k-mer counts for individual sequences in a fasta file.