kbo-cli

Command-line interface for the kbo local aligner.

Documentation is available at https://docs.rs/kbo.

Installation

Download

Binaries are available from the Releases page.

From bioconda

Run

conda install -c bioconda -y kbo-cli

Using cargo

Run cargo install kbo-cli.

Compile from source

Run

git clone https://github.com/tmaklin/kbo-cli
cd kbo-cli
cargo build --release

This will build the kbo executable in target/release/kbo directory.

Usage

kbo-cli provides access to three main operations:

• kbo call calls single and multi base substitutions, insertions, and deletions in a query sequence against a reference and reports their positions and sequences. Call is useful for problems that require .vcf files.
• 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.
• 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 and ska map.

For usage instructions, see the documentation at https://docs.rs/kbo.

License

kbo-cli is dual-licensed under the MIT and Apache 2.0 licenses.