Nagakishore Jammula

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The Automata Processor is a new accelerator technology that supports direct hardware implementation of a set of non-deterministic finite automata over a streaming input, and is designed for complex string pattern matching applications. In this paper, we broaden the scope of this architecture beyond its primary design goal, by developing algorithmic(More)
Genome sequencing, using instruments in vogue today, deciphers in the order of a billion short genomic fragments per run. These fragments are a few hundred bases long and are commonly referred to as `reads'. Reads contain errors due to limitations of sequencing technology. Read error correction enhances the quality of results produced by applications in(More)
Virtualization allows the platform to have increased number of logical processors by multiplexing the underlying resources across different virtual machines. The hardware resources get time shared not only between different virtual machines, but also between different workloads of the same virtual machine. An important source of performance degradation in(More)
State-of-the-art high-throughput sequencing instruments decipher in excess of a billion short genomic fragments per run. The output sequences are referred to as 'reads'. These read datasets facilitate a wide variety of analyses with applications in areas such as genomics, metagenomics, and transcriptomics. Owing to the large size of the read datasets, such(More)
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