SRFAligner and SRFChainer are long-read alignment tools based on indexable Elastic Founder Graphs (iEFGs). iEFGs can be obtained from FASTA multiple sequence alignments using founderblockgraph, or from a VCF file with the pipeline implemented in experiments/vcf-to-hapl-to-efg using founderblockgraph and vcf2multialign. The graphs used in the experiments can be found at doi.org/10.5281/zenodo.14012881.
SRFAligner and SRFChainer depend on efg-locate, chainx-block-graph, and GraphAligner. To clone this repository and compile the first two:
git clone https://github.com/algbio/SRFAligner && cd SRFAligner
git submodule update --init tools/{sdsl-lite-v3,concurrentqueue}
make
and GraphAligner's executable is expected to be found in folder tools/GraphAligner/bin, so you can run command git submodule update --init --recursive tools/GraphAligner and follow its compilation instructions. If GraphAligner is already installed in your system, you can just modify the relative line in SRFAligner and SRFChainer:
sed --in-place '7s/.*/graphaligner=GraphAligner/' SRFAligner
sed --in-place '7s/.*/graphaligner=GraphAligner/' SRFChainer
sed --in-place '7s/.*/graphaligner=GraphAligner/' efg-memsAligner
Finally, to use MEM seeds computed by efg-mems, efg-memsAligner expects efg-mems's executable to be in tools/efg-mems/efg-mems:
git submodule update --init --recursive tools/efg-mems
cd tools/efg-mems/sdsl-lite
./install.sh .
cd ..
cmake .