CUSHAW (the first release of CUSHAW software package for next-generation sequencing read alignment) is a CUDA compatible short read alignment algorithm for multiple GPUs sharing a single host. This aligner is designed based on the Burrows-Wheeler transform (BWT) and programmed using CUDA C++ parallel programming language. Performance evaluation, using simulated as well as real short read datasets, reveals that our aligner 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. This algorithm is presented in the publication " CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform".
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