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`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. | ||
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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``` | ||
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`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``` | ||
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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. |