A Variant of Parallel Plane Sweep Algorithm for Multicore Systems

Khlopotine, Andrei B.; Jandhyala, Vikram; Kirkpatrick, Desmond A.

doi:10.1109/tcad.2013.2245940

Cited by 11 publications

(4 citation statements)

References 9 publications

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“…To address these shortcomings, we developed a parallel algorithm that concurrently chrom-sweeps “chunks” of query and database intervals. Unlike previous in-memory parallel sweeping methods that uniformly partition the input [ 15 ], we define (without the need for preprocessing [ 16 ]) chunks by consecutive query intervals that meet one of two criteria: either the set reaches the “chunk size” threshold or the genomic distance to the next interval exceeds the “gap size” threshold. Restricting the chunk size creates reasonably even work among the threads to support efficient load balancing (i.e., to avoid task divergence).…”

Section: Methodsmentioning

confidence: 99%

Vcfanno: fast, flexible annotation of genetic variants

2016

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The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel “chromosome sweeping” algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0973-5) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Vcfanno: fast, flexible annotation of genetic variants

2016

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“…Parallel algorithm developed by McKenney et al and their OpenMP implementation is targeted towards multicore CPUs and it is not fine-grained to exploit the SIMT parallelism in GPUs [11,8,9]. Contrary to the abovementioned parallel algorithm, our algorithm is targeted to GPU and achieves higher speedup.…”

Section: Existing Work On Parallelizing Segment Intersection Algorithmsmentioning

confidence: 99%

OpenACC Based GPU Parallelization of Plane Sweep Algorithm for Geometric Intersection

Paudel

Puri

2019

Accelerator Programming Using Directives

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“…To address these shortcomings, we developed a parallel algorithm that concurrently chromsweeps "chunks" of query and database intervals. Unlike previous in-memory parallel sweeping methods that uniformly partition the input [15], we define (without the need for preprocessing [16]) chunks by consecutive query intervals that meet one of two criteria: either the set reaches the "chunk size" threshold, or the genomic distance to the next interval exceeds the "gap size" threshold. Restricting the chunk size creates reasonably even work among the threads to support efficient load balancing (i.e., to avoid task divergence).…”

Section: A Parallel Chrom-sweep Algorithmmentioning

confidence: 99%

Vcfanno: fast, flexible annotation of genetic variants

Pedersen

Layer

Quinlan

2016

Preprint

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The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license.

show abstract

A Variant of Parallel Plane Sweep Algorithm for Multicore Systems

Cited by 11 publications

References 9 publications

Vcfanno: fast, flexible annotation of genetic variants

Vcfanno: fast, flexible annotation of genetic variants

OpenACC Based GPU Parallelization of Plane Sweep Algorithm for Geometric Intersection

Vcfanno: fast, flexible annotation of genetic variants

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