This app contains benchmarks for various core algorithms and data structures implemented in SeqAn.
- Indices
- Construction
- Top-down traversal
- Exact and approximate string matching
- Filters
- q-Grams
- Non-overlapping seeds
Download the SeqAn library:
git clone https://github.com/seqan/seqan.git
Download the bench app into the SeqAn apps folder:
git clone https://github.com/esiragusa/bench.git seqan/apps/bench
Create a Makefile project:
mkdir seqan-build
cd seqan-build
cmake ../seqan -DCMAKE_C_COMPILER=/usr/bin/gcc-4.8 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.8
List all Makefile targets of the bench app:
make help | grep bench_
Build e.g. the index construction benchmark:
make bench_construct
To get a complete usage description, invoke each tool with -h or --help.
For questions or comments, feel free to contact: Enrico Siragusa <[email protected]>