Yara – Yet another read aligner

Yara is an exact tool for aligning DNA sequencing reads to reference genomes.

Main features:

  • Exhaustive enumeration of sub-optimal end-to-end alignments under the edit distance.
  • Excellent speed, memory footprint and accuracy.
  • Accurate mapping quality computation.
  • Support for reference genomes consisiting of million of contigs.
  • Direct output in SAM/BAM format.

Supported data: Yara has been tested on DNA reads (i.e., Whole Genome, Exome, ChIP-seq, MeDIP-seq) produced by the following sequencing platforms:

  • Illumina GA II, HiSeq and MiSeq (single-end and paired-end).
  • Life Technologies Ion Torrent Proton and PGM.

Quality trimming is necessary for Ion Torrent reads and recommended for Illumina reads.

Unsupported data:

  • RNA-seq reads spanning splicing sites.
  • Long noisy reads (e.g., Pacific Biosciences RSII, Oxford Nanopore MinION).


  • Download binaries
  • View source code and REAMDE on GitHub (It is strongly recommended to compile Yara from sources)
  • Yara is the follow-up of the Masai project. Use of Masai is discouraged. Nonetheless, old Masai binaries can still be downloaded here.

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