DIAMOND

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

SIMD C library for global, semi-global, and local pairwise sequence alignments

A system for rapidly aligning entire genomes, whether in complete or draft form.