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Recently, redundant network traffic elimination has attracted a lot of attention from both the academia and the industry. A core challenge and enabling technique in implementing redundancy elimination is to perform content-based chunking, which typically involves the computationally heavy Rabin fingerprinting algorithm. In this paper, we propose a GPU-based implementation of Rabin fingerprinting to...
The suffix array and Burrows-Wheeler Transform are critical index structures in next generation sequence analysis. The construction of such index structures for mammalian-sized genomes can take thousands of seconds (i.e. tens of minutes). Its construction is complicated by computational overheads that coming from irregular or complex memory-access patterns. This paper rigorously characterizes the...
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