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 files, have a look at https://github.com/christopher-schroeder/rust-htslib.

Resources

• Homepage: https://github.com/johanneskoester/rust-bio
• API documentation: https://johanneskoester.github.io/rust-bio
• Continuous integration tests: https://travis-ci.org/johanneskoester/rust-bio
• Roadmap: https://github.com/johanneskoester/rust-bio/issues/3

Usage

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

toml [dependencies] bio = "*"

and import the crate from your source code:

```rust 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/doc/bio/index.html

Authors

• Johannes Köster (johannes.koester@tu-dortmund.de)
• Christopher Schröder (christopher.schroeder@uni-due.de)
• Peer Aramillo Irizar

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.