High-performance genome sorting program

This paper is devoted to the practical application of parallel sorting algorithms and parallel input-output methods for the problem of genome alignment. The paper considers different approaches to the implementation of such algorithms, taking into account the capabilities of high-performance systems...

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Published inProcedia computer science Vol. 193; pp. 464 - 473
Main Authors Kasilov, Vasily, Drobintsev, Pavel, Voinov, Nikita
Format Journal Article
LanguageEnglish
Published Elsevier B.V 2021
Subjects
alignment
BAM
genome
HPC
OpenMP
SAM files
sorting algorithm
SAM files
genome
OpenMP
HPC
sorting algorithm
alignment
BAM
Online AccessGet full text
ISSN1877-0509
1877-0509
DOI10.1016/j.procs.2021.10.048

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Abstract This paper is devoted to the practical application of parallel sorting algorithms and parallel input-output methods for the problem of genome alignment. The paper considers different approaches to the implementation of such algorithms, taking into account the capabilities of high-performance systems. Main purpose of the work is to develop a genome sorting program, the efficiency of which significantly exceeds the efficiency of free software analogues. The genome sorting program is implemented for a supercomputer using the C++ language and the OpenMP and OpenMPI. The developed program demonstrates a significant increase in the speed of operation (up to 10 times) compared to free software analogues due to massive parallel data input and output. Different approaches for data input/output parallelization and data processing considered in the paper can be applied in other subject areas.
AbstractList This paper is devoted to the practical application of parallel sorting algorithms and parallel input-output methods for the problem of genome alignment. The paper considers different approaches to the implementation of such algorithms, taking into account the capabilities of high-performance systems. Main purpose of the work is to develop a genome sorting program, the efficiency of which significantly exceeds the efficiency of free software analogues. The genome sorting program is implemented for a supercomputer using the C++ language and the OpenMP and OpenMPI. The developed program demonstrates a significant increase in the speed of operation (up to 10 times) compared to free software analogues due to massive parallel data input and output. Different approaches for data input/output parallelization and data processing considered in the paper can be applied in other subject areas.
Author Kasilov, Vasily
Voinov, Nikita
Drobintsev, Pavel
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Cites_doi 10.15690/vramn1108
10.1093/nar/gkp1137
10.1038/nrd.2017.226
10.1007/s12575-009-9004-1
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Keywords SAM files
genome
OpenMP
HPC
sorting algorithm
alignment
BAM
Language English
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StartPage 464
SubjectTerms alignment
BAM
genome
HPC
OpenMP
SAM files
sorting algorithm
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Title High-performance genome sorting program
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