lh3/minibwa

A fast and sensitive gapped read aligner

Aligns short reads using dynamic seed size with strobemers

Graph-based alignment (Hierarchical Graph FM index)

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

SPAdes Genome Assembler

base-accurate DNA sequence alignments using WFA and mashmap3

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling