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,
• a convenient alphabet implementation,
• 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 and BED readers and writers.

For reading and writing BAM and BCF 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;

// Import some modules use bio::alphabets; use bio::datastructures::suffixarray::suffixarray; use bio::datastructures::bwt::bwt; use bio::data_structures::fmindex::FMIndex; use bio::io::fastq;

// Create an FM-Index for a given text. let alphabet = alphabets::dna::iupacalphabet(); let pos = suffixarray(text); let bwt = bwt(text, &pos); let fmindex = FMIndex::new(&bwt, 3, &alphabet);

// Iterate over a FASTQ file, use the alphabet to validate read // sequences and search for exact matches in the FM-Index. let reader = fastq::Reader::fromfile("reads.fastq"); for record in reader.records() { let seq = record.seq(); if alphabet.isword(seq) { let interval = fmindex.backward_search(seq.iter()); let positions = interval.occ(&pos); } } ```

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

Author

Johannes Köster (koester@jimmy.harvard.edu)

Contributors

• 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.