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fix: make minor fixes to README
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suchapalaver committed Sep 24, 2023
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# `krust`
# `krust`: counts k-mers, written in rust

## 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).
`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
Usage: krust <k> <path> [reader]
krust: counts k-mers, written in rust

Usage: krust <k> <path>

Arguments:
<k> provides k length, e.g. 5
<path> path to a FASTA file, e.g. /home/lisa/bio/cerevisiae.pan.fa
[reader] select *rust-bio* or *needletail* as FASTA reader [default: rust-bio]
<k> provides k length, e.g. 5
<path> 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.
`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:

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