Yara is an exact tool for aligning DNA sequencing reads to reference genomes.
- 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.
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.
- RNA-seq reads spanning splicing sites.
- Long noisy reads (e.g., Pacific Biosciences RSII, Oxford Nanopore MinION). Previous applications:
Yara is the follow-up of the Masai project. Use of Masai is discouraged. Nonetheless, old Masai binaries can still be downloaded here.
- E. Siragusa, D. Weese, K. Reinert, “Fast and accurate read mapping with approximate seeds and multiple backtracking”, vol. 41, iss. 7, 2013-01-28.
- Enrico Siragusa, “Approximate string matching for high-throughput sequencing”, p. 127, 2015-07-23.