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Benjamin Buchfink, Chao Xie, and D. H Huson (2015)

Fast and Sensitive Protein Alignment using DIAMOND

Nature Methods, 12:59-60.

The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.
Published online 17 November 2014