Yara

Overview

Yara is yet another read aligner.

Main features

  • Reporting of optimal end-to-end alignments under the edit distance
  • Multi-core parallelization
  • Low memory footprint
  • Output in SAM or BAM format

Supported sequencing platforms

  • Illumina HiSeq and MiSeq
  • Life Technologies Ion Torrent Proton and PGM

Reads quality control and trimming is necessary for Ion Torrent reads yet recommended in general.

Supported sequencing protocols

  • DNA-seq
  • Exome-seq
  • ChIP-seq

Please, note that Yara does not support RNA-seq as it cannot map reads between intron-intron splicing sites.

Downloads

Yara 32 or 64 bits precompiled binaries for Linux, MacOS X and Windows can be downloaded by following the links below.


Yara sources are shipped within the SeqAn library and can be browsed here. Jump to the section Compilation from source code for instructions on how to compile Yara from sources.

Yara is the follow-up of the Masai read mapper. 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.

Compilation from source code

The following instructions assume Linux or MacOS X. For more information, including Windows instructions, follow also the SeqAn getting started tutorial.

A C++ compiler implementing the C++11 standard and OpenMP 3.0 extensions is necessary to build Yara from sources. If unsure, use GNU G++ 4.8 or newer. Note that the standard Clang++ 3.3 compiler shipped with MacOS X does not provide OpenMP extensions, thus it will build Yara without multi-core parallelization.

First download the latest SeqAn sources:

git clone https://github.com/seqan/seqan.git -b develop

Create a SeqAn build project in Release mode, using G++ 4.8 as compiler:

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

Compile Yara binaries:

make yara_indexer yara_mapper

After compilation, copy the binaries to a folder in your PATH, eg.:

sudo cp bin/yara_* /usr/local/bin

Usage

Please take a look at the README file for usage instructions.

Contact

For questions, comments, or suggestions feel free to contact Enrico Siragusa.

References

  1. Siragusa, E., Weese D., and Reinert, K. (2014). Yara: reliable read mapping at high-throughput sequencing speed. 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 16. July 2014