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).

Links

• 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.

Please Cite

• Siragusa, E., (2015). Approximate string matching for high-throughput sequencing. Free University of Berlin, 2015.
• 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.

Contact

For questions, comments, or suggestions please contact:

Enrico Siragusa
enrico.siragusa@fu-berlin.de