xp3i4/bench

SeqAn Benchmarks

SeqAn Benchmarks

This app contains benchmarks for various core algorithms and data structures implemented in SeqAn.

Benchmarks

• Indices
  • Construction
  • Top-down traversal
  • Exact and approximate string matching
• Filters
  • q-Grams
  • Non-overlapping seeds

Installation

1. Download the SeqAn library:

   git clone https://github.com/seqan/seqan.git

2. Download the bench app into the SeqAn apps folder:

   git clone https://github.com/esiragusa/bench.git seqan/apps/bench

3. 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

4. List all Makefile targets of the bench app:

   make help | grep bench_

5. Build e.g. the index construction benchmark:

   make bench_construct

Usage

To get a complete usage description, invoke each tool with -h or --help.

Contact

For questions or comments, feel free to contact: Enrico Siragusa <[email protected]>