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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,
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

[dependencies]
bio = "*"

and import the crate from your source code:

extern crate bio;

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

// Create an FM-Index for a given text.
let alphabet = alphabets::dna::iupac_alphabet();
let pos = suffix_array(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::from_file("reads.fastq");
for record in reader.records() {
    let seq = record.seq();
    if alphabet.is_word(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