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.
- clone this repository:
git clone --recurse-submodules https://github.com/seqan/stellar3 - create a build directory and visit it:
mkdir stellar3/build && cd $_ - run cmake:
cmake .. - build the application:
make - show the help page:
./bin/stellar --help
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.
