SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

SW#–GPU-enabled exact alignments on genome scale

(2013) Matija Korpar et al.   BIOINFORMATICS

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

(2013) Yongchao Liu et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH