https://github.com/seqan/dream-stellar
Fast and exact local alignments
https://github.com/seqan/dream-stellar
Last synced: 9 months ago
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Fast and exact local alignments
- Host: GitHub
- URL: https://github.com/seqan/dream-stellar
- Owner: seqan
- License: bsd-3-clause
- Created: 2021-07-09T07:55:13.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2025-06-19T08:17:54.000Z (about 1 year ago)
- Last Synced: 2025-06-19T09:29:34.889Z (about 1 year ago)
- Language: C++
- Homepage:
- Size: 4.85 MB
- Stars: 1
- Watchers: 3
- Forks: 2
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
Awesome Lists containing this project
README
# DREAM-Stellar [![install with bioconda][1]][2] [![build status][3]][4] [![codecov][5]][6]
[1]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat "Install with bioconda"
[2]: #install-with-bioconda-linux
[3]: https://img.shields.io/github/actions/workflow/status/seqan/dream-stellar/ci_linux.yml?branch=main&style=flat&logo=github&label=DREAM-Stellar%20CI "Open GitHub actions page"
[4]: https://github.com/seqan/dream-stellar/actions?query=branch%3Amain
[5]: https://codecov.io/gh/seqan/dream-stellar/branch/main/graph/badge.svg "Open Codecov page"
[6]: https://codecov.io/gh/seqan/dream-stellar
## Getting started
Find the set of local alignments between sets of reference and query sequences.
`dream-stellar build test/data/dream/ref.fasta --pattern 50 --output index.ibf`
`dream-stellar search --index index.ibf --query test/data/dream/query.fasta --error-rate 0.02 --output search.gff`
For a detailed list of options, see the help pages:
```console
dream-stellar --help
dream-stellar build --help
dream-stellar search --help
```
## Download and Installation
### Install with [bioconda](http://bioconda.github.io/recipes/dream-stellar/README.html) (Linux)
```bash
conda install -c bioconda -c conda-forge dream-stellar
```
### Download and compile from source
Prerequisites (click to expand)
* CMake >= 3.25
* GCC 10, 11 or 12 (most recent minor version)
* git
Refer to the [Seqan3 Setup Tutorial](https://docs.seqan.de/seqan/3-master-user/setup.html) for more in depth information.
Download current master branch (click to expand)
```bash
git clone https://github.com/seqan/dream-stellar
```
Building (click to expand)
```bash
cd dream-stellar
mkdir -p build
cd build
cmake ..
make
```
The binary can be found in `bin`.
You may want to add the executable to your PATH:
```
export PATH=$(pwd)/bin:$PATH
valik --version
```
## DREAM-Stellar benchmark
The DREAM-Stellar [benchmark](https://github.com/eaasna/DREAM-stellar-benchmark/tree/v2.0) contains example workflows for using DREAM-Stellar for distributed local alignment.
## Authorship and Copyright
DREAM-Stellar is licensed under BSD 3, for details please see the [license](https://github.com/seqan/dream-stellar/blob/main/LICENSE.md).