Yara – Yet another read aligner

Getting started

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:

mkdir seqan-build
cd seqan-build
cmake ../seqan -DCMAKE_BUILD_TYPE=Release \
               -DCMAKE_C_COMPILER=/usr/bin/gcc-4.8 \

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.


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.

Other downloads

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.


  1. Siragusa, E., Weese D., and Reinert, K. (2014). Yara: well-defined alignment of high-throughput sequencing reads. To appear.
  2. Siragusa, E., Weese D., and Reinert, K. (2013). Fast and accurate read mapping with approximate seeds and multiple backtrackingNucleic Acids Research2013, 1–8.
Last Update 26. January 2016