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This project contains the source code and openCL/GPU bench for the phageterm project. I will leave it to the authors (Marc and Julian) to describe it and will just talk of the openCL benchmark part.
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1. Mapping or reads
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In the original version of phageterm, mapping reads than randomly choosing a mapping position for each read took approximatiely 80% of the execution time. It was done with the regexp python package. I studied several possibilities to reduce execution time.
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* optimize regexp or use it differently
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I first thought to that by I didn't find anything relevant except compiling the regexp element which is not of any use since it changes with each read.
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* use another python package with special text searching algorithms.
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I thought of the Knuth Morris algorithm |
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