Raptor

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences

Download and Installation

See the documentation for detailed information on how to download, install, and compile Raptor.

There may be performance benefits when compiling from source, as Raptor can be optimized for the host system.

Install with bioconda (Linux)

conda install -c bioconda -c conda-forge raptor

Example Data and Usage

See the documentation for usage.

raptor --help will show available commands. Each command will have a respective help page that can be shown via, e.g., raptor build --help.

Authorship and Copyright

Raptor is being developed by Enrico Seiler, but also incorporates much work from other members of SeqAn.

Citation

In your academic works (also comparisons and pipelines) please cite:

• Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782
• Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries; Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron, and Knut Reinert; Genome Biol 24, 131 (2023). doi: https://doi.org/10.1186/s13059-023-02971-4

RECOMB 2021

Raptor was presented at the 25th International Conference on Research in Computational Molecular Biology:

• Slides
• Pre-recorded version of the talk

Please see the License section for information on allowed use.

Supplementary

The subdirectory util contains applications and scripts related to papers.

License

Raptor is open-source software. However, certain conditions apply when you (re-)distribute and/or modify Raptor, please see the license.

Sponsorships

We are grateful to Vercel for building and hosting our documentation, and they even provide preview builds within our pull requests. Check them out!