AC-DIAMOND

To speed up the alignment of DNA reads or assembled contigs against a protein database has been a challenge up to now. The recent tool DIAMOND has signicantly improved the speed of BLASTX and RAPSearch, with a similar degree of sensitivity. Yet for applications like metagenomics, where a large amount of data is involved, DIAMOND still takes too much time. We introduce AC-DIAMOND, which attempts to speed up DIAMOND via better SIMD parallelization and reference indexing. Experimental results show that AC-DIAMOND is about 4 times faster than DIAMOND on aligning DNA reads or contigs while retaining the essentially the same sensitivity.