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# kbo | ||
Spectral Burrows-Wheeler transform accelerated local alignment search. | ||
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kbo is an approximate local aligner based on converting [_k_-bounded matching | ||
statistics](https://www.biorxiv.org/content/10.1101/2024.02.19.580943v1) | ||
into a character representation of the underlying alignment sequence. | ||
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Documentation is available at [https://docs.rs/kbo](https://docs.rs/kbo). | ||
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## Installation | ||
kbo is distributed as three separate Rust packages: | ||
- [kbo](https://github.com/tmaklin/kbo) contains a Rust library implementing the core algorithm (this repository). | ||
- [kbo-cli](https://github.com/tmaklin/kbo-cli) provides a command-line interface for `kbo find` and `kbo map`. | ||
- [kbo-gui](https://github.com/tmaklin/kbo-cli) provides a WebAssembly graphical user interface for running kbo in the browser. | ||
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## About | ||
kbo supports two main operations: | ||
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- `kbo find` matches the _k_-mers in a query sequence with the | ||
reference and reports the local alignment segments found within the | ||
reference. Find is useful for problems that can be solved with | ||
[blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi). | ||
- `kbo map` maps the query sequence against a reference | ||
sequence, and reports the nucleotide sequence of the alignment relative to | ||
the reference. Map solves the same problem as | ||
[snippy](https://github.com/tseemann/snippy) and [ska | ||
map](https://docs.rs/ska/latest/ska/#ska-map). | ||
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kbo uses the [Spectral Burrows-Wheeler | ||
Transform](https://docs.rs/sbwt/latest/sbwt/) data structure that allows | ||
efficient _k_-mer matching between a target and a query sequence and | ||
fast retrieval of the _k_-bounded matching statistic for each _k_-mer match. | ||
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## License | ||
kbo is dual-licensed under the [MIT](LICENSE-MIT) and [Apache 2.0](LICENSE-APACHE) licenses. |