STELLAR3 - the SwifT Exact LocaL AligneR

This is similar to STELLAR but uses the sharg parser 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 for details on the Stellar output formats.