Acceleration of short and long DNA read mapping without loss of accuracy using suffix array by Joaquín Tárraga, et al. (Bioinformatics (2014) doi: 10.1093/bioinformatics/btu553)
Abstract:
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20x for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current, state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.
Always nice to see an old friend, suffix arrays, in the news!
Source code: https://github.com/opencb/hpg-aligner.
For documentation and software: http://wiki.opencb.org/projects/hpg/doku.php?id=aligner:overview
I first saw this in a tweet by Bioinfocipf.