Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
“suchapalaver” committed May 7, 2022
1 parent 8091633 commit 2b4cb13
Showing 1 changed file with 5 additions and 7 deletions.
12 changes: 5 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
`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--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](https://en.wikipedia.org/wiki/Complementarity_(molecular_biology)#DNA_and_RNA_base_pair_complementarity)) and their frequency across all records in the given 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:
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```
Expand All @@ -12,8 +12,6 @@ or, searching for kmers of length 21:
```(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).

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.
`krust` uses the [`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) Rust libraries.

* Unusual, yes, to provide this data in the repo, but it's helped me spread word about what I'm doing.

0 comments on commit 2b4cb13

Please sign in to comment.