Fast and Sensitive Protein Alignment Using DIAMOND

Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17.

Abstract

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Humans
  • Metagenomics / methods*
  • Microbiota / genetics
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA
  • Software*