GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units

(2018) Shanshan Ren et al.   Evolutionary Bioinformatics

CUDAlign 4.0: Incremental Speculative Traceback for Exact Chromosome-Wide Alignment in GPU Clusters

(2016) Edans Flavius de Oliveira Sandes et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

SW#–GPU-enabled exact alignments on genome scale

(2013) Matija Korpar et al.   BIOINFORMATICS

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

(2011) Jacek Blazewicz et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Highly Parameterized and Efficient FPGA-Based Skeleton for Pairwise Biological Sequence Alignment

(2009) K. Benkrid et al.   IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS