https://github.com/suchapalaver/krust

Bioinformatics 101 tool for counting unique k-length substrings in DNA
https://github.com/suchapalaver/krust

beginner-friendly bioinformatics bioinformatics-tool bitpacking bytes clap dashmap genomics insta k-mer k-mer-counting k-mers kmer kmer-counting kmers needletail parallelization rayon rust rust-bio

Last synced: 11 days ago
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Bioinformatics 101 tool for counting unique k-length substrings in DNA

• Host: GitHub
• URL: https://github.com/suchapalaver/krust
• Owner: suchapalaver
• License: mit
• Created: 2021-09-06T18:32:57.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2023-09-25T02:11:52.000Z (about 1 year ago)
• Last Synced: 2024-10-13T13:28:58.885Z (25 days ago)
• Topics: beginner-friendly, bioinformatics, bioinformatics-tool, bitpacking, bytes, clap, dashmap, genomics, insta, k-mer, k-mer-counting, k-mers, kmer, kmer-counting, kmers, needletail, parallelization, rayon, rust, rust-bio
• Language: Rust
• Homepage:
• Size: 23.1 MB
• Stars: 30
• Watchers: 0
• Forks: 5
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# `krust`: counts k-mers, written in rust

`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. `krust` is 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 data. `krust` is tested for accuracy against [jellyfish](https://github.com/gmarcais/Jellyfish).

```bash

krust: counts k-mers, written in rust

Usage: krust  

Arguments:

       provides k length, e.g. 5

    path to a FASTA file, e.g. /home/lisa/bio/cerevisiae.pan.fa

Options:

  -h, --help     Print help information

  -V, --version  Print version information

```

`krust` supports either `rust-bio` or `needletail` to read FASTA record. Use the `--features` flag to select.  

Run `krust` with `rust-bio`'s fasta reader to count *5*-mers like this:

```bash

cargo run --release --features rust-bio -- 5 your/local/path/to/fasta_data.fa

```

or, searching for *21*-mers with `needletail` as the fasta reader, like this:  

```bash

cargo run --release --features needletail -- 21 your/local/path/to/fasta_data.fa

```

`krust` prints to `stdout`, writing, on alternate lines:

```bash

>114928

ATGCC

>289495

AATCA

...

```