10 releases (5 breaking)
0.8.0 | May 11, 2024 |
---|---|
0.7.1 | Jun 15, 2023 |
0.7.0 | Feb 3, 2023 |
0.6.1 | Feb 1, 2023 |
0.1.0 | Jan 9, 2018 |
#178 in Biology
580 downloads per month
30KB
532 lines
A read aligner for aligned sequences
Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. The main use case is through SingleM, although it can be used independently without issue to search and cluster other pre-aligned sequences.
Installation
Installation through bioconda
If you have bioconda installed:
conda install -c bioconda smafa
Installation through Cargo
Smafa can be installed in the usual way Rust packages are installed. After installing Rust, smafa can be installed using cargo:
cargo install smafa
Usage
To run the aligner, first make a db with smafa makedb
and then query that
database with smafa query
. To see how to use these modes, use e.g. smafa query --help
.
Help
If you have any questions or comments, please raise an issue on the GitHub repository, or just email Ben Woodcroft.
License
Smafa is developed by the Woodcroft lab at the Centre for Microbiome Research, School of Biomedical Sciences, QUT. It is licensed under GPL3 or later.
The code is available at https://github.com/wwood/smafa.
Dependencies
~7–17MB
~240K SLoC