This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Rust
holtgrewe and johanneskoester Adding missing constructors on HMM-related types. (#181)
The iterators must be constructable for implementing models outside
of rust-bio.
Latest commit 74f7db7 Jul 12, 2018

README.md

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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.

Please see the homepage for examples and documentation.

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,
  • utilities to work with PSSMs,
  • an orf research algorithm,
  • a rank/select data structure,
  • serde support for all data structures when built with nightly feature,
  • FASTQ and FASTA and BED readers and writers,
  • helper functions for combinatorics and dealing with log probabilities.

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

Author

Johannes Köster

Contributors

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 introduce yourself here, 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.