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31 lines
1.5 KiB
Markdown
31 lines
1.5 KiB
Markdown
3 years ago
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---
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title: Porting and Benchmarking of BWAKIT pipeline on Open POWER architecture
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link:
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tags:
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- software
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- hardware
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- power8
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- genomemapping
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date: 2017-09-20
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draft: false
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---
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This paper describes how to port various pre-built application binaries used in BWAKIT into OpenPOWER architecture and
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execute the BWAKIT pipeline successfully.
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Next Generation Sequencing (NGS) technology produces large volume of genome data,
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which gets processed using various open source Bioinformatics tools.
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The configuration and compilation of some of the bioinformatics tools (e.g. BWAKIT, root) are challenging,
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requiring application porting for some architectures (e.g. IBM Power).
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Moreover, the application porting should not change the semantics of the program and output generated
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from different architectures should be similar across different architectures.
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Burrows-Wheeler Aligner (BWA) is the most popular genome mapping application used in BWAKIT toolset.
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The BWAKIT provides pre-compiled binaries for x86_64 architecture and end-to-end solution for genome mapping.
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This paper describes how to port various pre-built application binaries used in BWAKIT into OpenPOWER architecture and
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execute the BWAKIT pipeline successfully.
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In addition, it reports the validation of the output results on OpenPOWER to confirm the successful porting of BWAKIT.
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_Note: This paper is the result of collaboration within members of the Personalized Medicine Workgroup and Sidra medical and Research Center._
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