Clone testing repository:
git clone --recurse-submodules [email protected]:eaasna/DREAM-stellar-benchmark.git
Build data simulation library:
cd DREAM-stellar-benchmark/lib/raptor_data_simulation
mkdir build && cd build
cmake ../
make
You might need to copy the mason_genome binary into the raptor_data_simulation/build/bin directory.
cd ../
cp build/src/mason2/src/mason2-build/bin/mason_genome build/bin/mason_genome
Build valik prefilter and add binaries to $PATH: https://github.com/eaasna/valik
Other requirements:
- Biopython https://biopython.org/wiki/Packages
Create partially overlapping segments from the reference sequence.
valik split dmel.fasta --reference-output reference-metadata.txt --segment-output reference-segments.txt --overlap 151 --bins 1024
Build an IBF so that each segment corresponds to a bin.
valik build dmel.fasta --output index.ibf --size 8m --from-segments --seg-path reference-segments.txt --ref-meta reference-metadata.txt
Search the simulated reads in the IBF.
valik search --threads 8 --index index.ibf --query reads_e2_150/dmel.fastq --output search.out --error 1 --pattern 50 --overlap 5
- Simulated metagenomic data and a dataset from the bovine gut (https://omics.informatics.indiana.edu/mg/RAPSearch2/)
- D. melanogaster reference genome and simulated reads