PyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

ABSTRACT:

Background

Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python.

Results

The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provi

SUBMITTER: Warris S 

PROVIDER: S-EPMC5749749 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature