Pair-End Inexact Mapping on Hybrid GPU Environments and Out-Of-Core Indexes

Author(s): José Salavert, Andrés Tomás, Ignacio Medina, Kunihiko Sadakane, Ignacio Blanquer.

Journal Name: Current Bioinformatics

Volume 11 , Issue 4 , 2016

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Graphical Abstract:


Due to the NGS data deluge, sequence mapping has become an intensive task that, depending on the experiment, may demand high amounts of computing power or memory capacity.

On the one hand, GPGPU architectures have become a cost-effective solution that outperforms common processors in specific tasks. On the other hand, out-of-core implementations allow to directly access data from secondary memory, which may be useful when mapping against big indexes in systems with low memory configurations. In this paper we discuss the implementation of backward search methods for inexact mapping in these two different study cases.

A hybrid CPU-GPU implementation of a backward search algorithm capable of obtaining the pair-ends and the one error mappings of a read has been developed. This implementation can be used to increase the sensitivity and reduce the number of reads to be analysed with a dynamic programming approach.

Also, a CPU out-of-core index using MMAP has been studied (provided by csalib). Such index can be used in memory limited scenarios, in which the time of loading many different big genomes into memory is greater than the time needed to map the reads.

Keywords: Inexact Mapping, Burrows-Wheeler, FM-Index, Suffix Array, GPU, MMAP.

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Article Details

Year: 2016
Page: [459 - 469]
Pages: 11
DOI: 10.2174/1574893611666160212235359
Price: $65

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