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A dynamic pipeline for RNA sequencing on multicore processors

Authors:

Enrique S. Quintana-OrtíAuthors Info & Claims

EuroMPI '13: Proceedings of the 20th European MPI Users' Group Meeting

Pages 235 - 240

https://doi.org/10.1145/2488551.2488581

Published: 15 September 2013 Publication History

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Abstract

We present a concurrent algorithm for mapping short and long RNA sequences on multicore processors. Our solution processes the data, initially stored on disk, in batches of reads which are passed between the consecutive stages of a pipeline. A major operational reorganization of the original static pipeline, combined with a complete reimplementation based on POSIX threads, renders a dissociated execution between threads and stages/task types, so that threads can compute any type of pending task resulting in a dynamic pipeline. The experiments on a multicore platform reveal that this reorganization yields significantly higher performance, specially for architectures equipped with a small to moderate number of cores.

As an additional contribution, our experiments also reveal that the use of 16-nucleotide (nt) seeds during the one of the stages of the pipeline, instead of the 15-nt length that was proposed originally, yields a remarkable reduction in the execution time of the global alignment process while maintaining the sensitivity of the algorithm.

References

[1]

D. Adjeroh, T. C. Bell, and A. Mukherjee. The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern matching. Springer, 2008.

Digital Library

Google Scholar

[2]

L. Ben and S. Steven L. Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4):357--359, 2012.

Crossref

Google Scholar

[3]

R. Blumofe and C. Leiserson. Scheduling multithreaded computations by work stealing. In Proceedings of the 35th Annual Symposium on Foundations of Computer Science, Santa Fe, New Mexico, pages 356--368, November 1994.

Digital Library

Google Scholar

[4]

M. Garber, M. G. Grabherr, M. Guttman, and C. Trapnell. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature methods, 8:469--477, 2011.

Crossref

Google Scholar

[5]

J. L. Hennessy and D. A. Patterson. Computer Architecture: A Quantitative Approach. Morgan Kaufmann Pub., San Francisco, 5th edition, 2012.

Digital Library

Google Scholar

[6]

B. Langmead, C. Trapnell, M. Pop, and S. L Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology, 10(3):R25, 2009.

Crossref

Google Scholar

[7]

H. Li and N. Homer. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform, 11:473--483, 2010.

Crossref

Google Scholar

[8]

H. Martínez, J. Tárraga, I. Medina, S. Barrachina, M. Castillo, J. Dopazo, and E. S. Quintana-Ortí. Concurrent and accurate RNA sequencing on multicore platforms. Technical Report ICC 2013-03-01, Depto. Ingeniería y Ciencia de Computadores, Universidad Jaime I, Spain, 2013. Available at http://www.arxiv.org/1304.0681.

Google Scholar

[9]

OpenMP Architecture Review Board. OpenMP web site. http://www.openmp.org/.

Google Scholar

[10]

SAMtools. BAM/SAM API documentation. http://samtools.sourceforge.net/.

Google Scholar

[11]

T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. J. Mol. Biol., 147:195--197, 1981.

Crossref

Google Scholar

[12]

C. Trapnell, L. Pachter, and S. L. Salzberg. TopHat: discovering splice junctions with RNA-seq. Bioinformatics, 25(9):1105--1111, 2009.

Digital Library

Google Scholar

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Mascagni MIserte SMartínez HBarrachina SCastillo MMayo RPeña A(2019)Dynamic reconfiguration of noniterative scientific applicationsInternational Journal of High Performance Computing Applications10.1177/109434201880234733:5(804-816)Online publication date: 1-Sep-2019
https://dl.acm.org/doi/10.1177/1094342018802347
Al-Ghalith GMontassier EWard HKnights D(2016)NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated RibosomesPLOS Computational Biology10.1371/journal.pcbi.100465812:1(e1004658)Online publication date: 28-Jan-2016
https://doi.org/10.1371/journal.pcbi.1004658
Martínez HBarrachina SCastillo MTárraga JMedina IDopazo JQuintana-Ortí E(2016)A framework for genomic sequencing on clusters of multicore and manycore processorsThe International Journal of High Performance Computing Applications10.1177/109434201665324332:3(393-406)Online publication date: 22-Jun-2016
https://doi.org/10.1177/1094342016653243
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A dynamic pipeline for RNA sequencing on multicore processors

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Published In

EuroMPI '13: Proceedings of the 20th European MPI Users' Group Meeting

September 2013

289 pages

ISBN:9781450319034

DOI:10.1145/2488551

General Chair:
Jack Dongarra
University of Tennessee
,
Program Chairs:
Javier Garcia Blas
University Carlos III, Spain
,
Jesus Carretero
University Carlos III, Spain

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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SIGHPC: ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing

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Published: 15 September 2013

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EuroMPI '13: 20th European MPI Users's Group Meeting

September 15 - 18, 2013

Madrid, Spain

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EuroMPI '13 Paper Acceptance Rate 22 of 47 submissions, 47%;

Overall Acceptance Rate 66 of 139 submissions, 47%

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Mascagni MIserte SMartínez HBarrachina SCastillo MMayo RPeña A(2019)Dynamic reconfiguration of noniterative scientific applicationsInternational Journal of High Performance Computing Applications10.1177/109434201880234733:5(804-816)Online publication date: 1-Sep-2019
https://dl.acm.org/doi/10.1177/1094342018802347
Al-Ghalith GMontassier EWard HKnights D(2016)NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated RibosomesPLOS Computational Biology10.1371/journal.pcbi.100465812:1(e1004658)Online publication date: 28-Jan-2016
https://doi.org/10.1371/journal.pcbi.1004658
Martínez HBarrachina SCastillo MTárraga JMedina IDopazo JQuintana-Ortí E(2016)A framework for genomic sequencing on clusters of multicore and manycore processorsThe International Journal of High Performance Computing Applications10.1177/109434201665324332:3(393-406)Online publication date: 22-Jun-2016
https://doi.org/10.1177/1094342016653243
Martínez HBarrachina SCastillo MTárraga JMedina IDopazo JQuintana-Ortí E(2015)Scalable RNA Sequencing on Clusters of Multicore ProcessorsProceedings of the 2015 IEEE Trustcom/BigDataSE/ISPA - Volume 0310.1109/Trustcom.2015.631(190-195)Online publication date: 20-Aug-2015
https://dl.acm.org/doi/10.1109/Trustcom.2015.631
Martinez HTarraga JMedina IBarrachina SCastillo MDopazo JQuintana-Orti E(2015)Concurrent and Accurate Short Read Mapping on Multicore ProcessorsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2015.239207712:5(995-1007)Online publication date: 1-Sep-2015
https://dl.acm.org/doi/10.1109/TCBB.2015.2392077

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