CUSHAW - CUDA compatible short read alignment

CUSHAW has evolved into a software package for next-generation sequencing (NGS) read alignment.

CUSHAW (Release 1.x) is a CUDA compatible short read alignment algorithm to large genomes based on the Burrows-Wheeler transform (BWT), programmed using CUDA C++ parallel programming language. Performance evaluation, using simulated as well as real short read datasets, reveals that our algorithm running on one or two graphics processing units (GPUs) achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments, compared to three popular BWT-based aligners: Bowtie, BWA and SOAP2.

This aligner only provides support for ungapped alignment and has been incorporated to NVIDIA Tesla Bio Workbench
CUSHAW2 (Release 2.x) is a fast and high-throughput gapped read alignment, optimzied for multiple CPU cores using multi-threading.