https://github.com/seqan/stellar3
the SwifT Exact LocaL AligneR
https://github.com/seqan/stellar3
Last synced: 5 months ago
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the SwifT Exact LocaL AligneR
- Host: GitHub
- URL: https://github.com/seqan/stellar3
- Owner: seqan
- License: other
- Created: 2023-02-08T13:12:08.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-12-12T15:24:26.000Z (over 1 year ago)
- Last Synced: 2025-07-13T05:40:36.548Z (12 months ago)
- Language: C++
- Size: 147 MB
- Stars: 0
- Watchers: 4
- Forks: 2
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# STELLAR3 - the SwifT Exact LocaL AligneR
This is similar to [STELLAR](https://github.com/seqan/seqan/tree/master/apps/stellar) but uses the [sharg parser](https://docs.seqan.de/seqan3/3-master-user/tutorial_argument_parser.html) and can be used to narrow the search to only a segment of the reference database.
## Building Stellar3:
1. clone this repository: `git clone --recurse-submodules https://github.com/seqan/stellar3`
2. create a build directory and visit it: `mkdir stellar3/build && cd $_`
3. run cmake: `cmake ..`
4. build the application: `make`
5. show the help page: `./bin/stellar --help`
## Running Stellar3:
The `example` folder contains example data for a test run. Stellar3 can be used to produce soft-clipped read alignments or to find all local alignments between two genomes.
Searching the reference sequences for local alignments with a minimum length of 50 and a maximum error rate of 0.02:
`./bin/stellar -e 0.02 -l 50 -o mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`
Searching only a segment of the reference for local alignments:
`./bin/stellar --sequenceOfInterest 0 --segmentBegin 5000 --segmentEnd 7500 -e 0.02 -l 50 -o segment.mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`
Finding all local alignments between two related genomes:
`./bin/stellar -e 0.1 -l 50 -o alignments.gff ../example/NC_001474.fasta ../example/NC_001477.fasta`
See the original [documentation](https://github.com/seqan/seqan/tree/main/apps/stellar) for details on the Stellar output formats.