From fe64a38da4913d345a06ac144fc6bb8af3f47338 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tommi=20M=C3=A4klin?= Date: Mon, 18 Nov 2024 14:29:04 +0200 Subject: [PATCH] Update README. --- README.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/README.md b/README.md index b48b344..0d4be61 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,35 @@ # kbo Spectral Burrows-Wheeler transform accelerated local alignment search. +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. + +Documentation is available at [https://docs.rs/kbo](https://docs.rs/kbo). + +## 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. + +## About +kbo supports two main operations: + +- `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). + +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. + ## License kbo is dual-licensed under the [MIT](LICENSE-MIT) and [Apache 2.0](LICENSE-APACHE) licenses.