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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
[]
= "*"
and import the crate from your source code:
extern crate bio;
// Import some modules
use alphabets;
use suffix_array;
use bwt;
use FMIndex;
use fastq;
// Create an FM-Index for a given text.
let alphabet = iupac_alphabet;
let pos = suffix_array;
let bwt = bwt;
let fmindex = new;
// Iterate over a FASTQ file, use the alphabet to validate read
// sequences and search for exact matches in the FM-Index.
let reader = from_file;
for record in reader.records
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.