AC-DIAMOND v1: Accelerating large-scale DNA-protein alignment.

Abstract

SUMMARY: AC-DIAMOND (v1) is a DNA-protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed up the matching between query and reference sequences; second, adopting a compact form of dynamic programming to fully utilize the parallelism of the SIMD capability. AVAILABILITY: Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/. CONTACT: hjmai@cs.hku.hk, hfting@cs.hku.hk, twlam@cs.hku.hk. SUPPLEMENTARY INFORMATION: Benchmark data & results https://sourceforge.net/projects/ac-diamond-v1/files/data/.