Yara – Yet another read aligner
The following instructions assume Linux or OS X. For more information, including Windows instructions, refer to the SeqAn getting started tutorial.
Download the sources
Yara sources are shipped within the SeqAn library and can be browsed on GitHub.
Download the latest SeqAn sources:
git clone https://github.com/seqan/seqan.git -b develop
Create a build project
To build Yara, a C++11 compiler with OpenMP 3.0 extensions is required. If unsure, use GNU G++ 4.8 or newer.
Create a SeqAn build project in Release mode:
cmake ../seqan -DCMAKE_BUILD_TYPE=Release \
If the binaries are going to be executed on a different CPU type, disable architecture-specific optimizations. Note that this has an impact on Yara’s performance.
cmake . -DYARA_ARCH_NATIVE=OFF
Build and install
Make Yara binaries:
make yara_indexer yara_mapper
Copy the binaries to a folder in your PATH, eg.:
sudo cp bin/yara_* /usr/local/bin
Please take a look at the README file for usage instructions.
It is strongly recommended to compile Yara from sources. Some precompiled binaries for Linux, MacOS X and Windows can be downloaded by following the links below.
Yara is the follow-up of the Masai project. Deprecated Masai binaries can still be downloaded by following the links below. Please, note that these versions of the software are not maintained anymore.
Old Masai sources can still be downloaded here
For questions, comments, or suggestions feel free to contact Enrico Siragusa.
- Siragusa, E., Weese D., and Reinert, K. (2014). Yara: well-defined alignment of high-throughput sequencing reads. To appear.
- Siragusa, E., Weese D., and Reinert, K. (2013). Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Research, 2013, 1–8.
Last Update 24. November 2014