DIAMOND is a high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity.
On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 times faster than BLASTX, finding more than 94% of all matches.
- Benjamin Buchfink, Chao Xie & Daniel H. Huson, Fast and Sensitive Protein Alignment using DIAMOND, Nature Methods, 12, 59–60 (2015) doi:10.1038/nmeth.3176.
- Video Introduction to Microbiome Analysis using DIAMOND + MEGAN.
See the DIAMOND github page: here.