bio 0.3.3

A rusty bioinformatics library. This library provides implementations of many algorithms and data structures that are useful for bioinformatics.
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Rust-Bio, a bioinformatics library for Rust.

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Currently, rust-bio provides

  • most major pattern matching algorithms,
  • pairwise alignment,
  • suffix arrays,
  • BWT and FM-Index,
  • FMD-Index for finding supermaximal exact matches,
  • a q-gram index,
  • a rank/select data structure,
  • FastQ and Fasta readers and writers.

For reading and writing BAM and BCF files, have a look at https://github.com/christopher-schroeder/rust-htslib.

Resources

Usage

To use rust-bio in your Rust project, add the following to your Cargo.toml

[dependencies]
bio = "*"

and import the crate from your source code:

extern crate bio;
// use e.g. a pattern matching algorithm
use bio::pattern_matching::bndm::BNDM;

let pattern = b"GAAAA";
let text = b"ACGGCTAGAAAAGGCTAGAAAA";
let bndm = BNDM::new(pattern);
let matches = bndm.find_all(text);

For more information, please read the API documentation: https://johanneskoester.github.io/rust-bio

Authors

The next name in this list could be you! If you are interested in joining the effort to build a general purpose Rust bioinformatics library, just send me an email, or issue a pull request with your first contribution.

License

Licensed under the MIT license http://opensource.org/licenses/MIT. This project may not be copied, modified, or distributed except according to those terms.