MELC Genomics: A Framework for De Novo Genome Assembly

Costa, Evaldo B.

doi:10.1089/cmb.2017.0102

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2020

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“…This technology, on the other hand, must process files that contain reads with a high percentage of errors (up to 15 %) [8] [13], requiring a large amount of repetitions of those reads and, consequently, a proportional increase in data volume and processing time.…”

Section: Introductionmentioning

confidence: 99%

DALIGNER Performance Evaluation on Intel Xeon Phi Architecture

Costa

Silva

Teixeira

EPiC Series in Computing

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In bioinformatics, DNA sequence assembly refers to the reconstruction of an original DNA sequence by the alignment and merging of fragments that can be obtained from several sequencing methods. The main sequencing methods process thousands or even millions of these fragments, which can be short (hundreds of base pairs) or long (thousands of base pairs) read sequences. This is a highly computational task, which usually requires the use of parallel programs and algorithms, so that it can be performed with desirable accuracy and within suitable time limits. In this paper, we evaluate the performance of DALIGNER long read sequences aligner in a system using the Intel Xeon Phi 7210 processor. We are looking for scalable architectures that could provide a higher throughput that can be applied to future sequencing technologies.

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Section: Introductionmentioning

confidence: 99%