Removing sequential bottlenecks in analysis of next-generation sequencing data

Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2014

Volumn , Issue , 2014, Pages 508-517

  Wang, Yi ^a   Agrawal, Gagan ^a   Ozer, Gulcin ^a   Huang, Kun ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Data Format Conversion; Next Generation Sequencing; Parallelization; Statistical Analysis

Indexed keywords

CHROMOSOMES; MEMORY ARCHITECTURE; STATISTICAL METHODS;

DATA FORMAT CONVERSION; DISTRIBUTED-MEMORY PARALLELISMS; FALSE DISCOVERY RATE; FORMAT CONVERSION; HIGH SCALABILITIES; NEXT-GENERATION SEQUENCING; PARALLELIZATIONS; SEQUENCE ALIGNMENTS;

DATA HANDLING;

EID: 84918808404     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPSW.2014.64     Document Type: Conference Paper

References (39)

1. Contrail: Assembly of Large Genomes using Cloud Computing. http://contrailbio. sourceforge.net.
2. Galaxy. http://galaxy.psu.edu/.
3. Jnomics. http://sourceforge.net/apps/mediawiki/jnomics/index.php.
4. Picard. http://picard.sourceforge.net.
5. BAM/SAM Specification, Sep 2011. v1.4-r985.
6. M. Baker. Next-generation sequencing: adjusting to data overload. Nature Methods, 7(7):495-499, Jul 2010.
7. D. W. Barnett, E. K. Garrison, A. R. Quinlan, M. Stromberg, and G. T. Marth. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12):1691-1692, 2011.
8. A. Buades, B. Coll, and J. M. Morel. A Non-Local Algorithm for Image Denoising. In 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05), volume 2 of CVPR '05, pages 60-65, Washington, DC, USA, June 2005. IEEE.
9. R. K. Dale, B. S. Pedersen, and A. R. Quinlan. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24):3423-3424, Dec. 2011.
10. J. Ekanayake, T. Gunarathne, and J. Qiu. Cloud Technologies for Bioinformatics Applications. IEEE Transactions on Parallel and Distributed Systems, 2011.
11. M. Gaggero and et al. Parallelizing bioinformatics applications with MapReduce. Cloud Computing and Its Applications, 2008.
12. R. C. Gentleman and et al. Bioconductor: open software development for computational biology and bioinformatics. Genome biology, 5(10):R80+, 2004.
13. B. Goossens, Q. Luong, J. Aelterman, A. Pizurica, and W. Philips. A GPUAccelerated Real-Time NLMeans Algorithm for Denoising Color Video Sequences. In J. Blanc-Talon, D. Bone, W. Philips, D. Popescu, and P. Scheunders, editors, Advanced Concepts for Intelligent Vision Systems, volume 6475 of Lecture Notes in Computer Science, pages 46-57. Springer Berlin / Heidelberg, 2010.
14. Z. Han, L. Tian, T. Pecot, T. Huang, R. Machiraju, and K. Huang. A signal processing approach for enriched region detection in RNA polymerase II ChIPseq data. BMC Bioinformatics, 13(Suppl 2):S2, 2012.
15. K. Huang, D. Zhang, and K. Wang. Non-local means denoising algorithm accelerated by GPU. In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7497, Oct. 2009.
16. C. A. Hutchison. DNA sequencing: bench to bedside and beyond. Nucleic Acids Research, 35(18):6227-6237, Sep 2007.
17. W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, and D. Haussler. The Human Genome Browser at UCSC. Genome Res, 12(6):996-1006, June 2002.
18. M. Kutlu and G. Agrawal. PAGE: A Framework for Easy PArallelization of GEnomic Applications. In Proceedings of IPDPS, 2014.
19. B. Langmead, K. D. Hansen, and J. T. Leek. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome biology, 11(8):R83+, Aug. 2010.
20. B. Langmead, M. C. Schatz, J. Lin, M. Pop, and S. L. Salzberg. Searching for SNPs with cloud computing. Genome biology, 10(11):R134+, Nov. 2009.
21. S. Leo, F. Santoni, and G. Zanetti. Biodoop: Bioinformatics on Hadoop. Parallel Processing Workshops, International Conference on, 0:415-422, 2009.
22. H. Li and R. Durbin. Fast and accurate short read alignment with burrowswheeler transform. Bioinformatics, 25(14):1754-1760, July 2009.
23. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England), 25(16):2078-2079, Aug. 2009.
24. E. Mardis. Next-Generation DNA Sequencing Methods. Annual Review of Genomics and Human Genetics, 9(1):387-402, June 2008.
25. A. Matsunaga, M. Tsugawa, and J. Fortes. CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications. eScience, IEEE International Conference on, 0:222-229, Dec. 2008.
26. A. McKenna and et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9):1297-1303, Sept. 2010.
27. M. Metzker. Emerging technologies in DNA sequencing. Genome Res, 15(12):1767-76, dec 2005.
28. M. Niemenmaa, A. Kallio, A. Schumacher, P. Klemelä, E. Korpelainen, and K. Heljanko. Hadoop-BAM: Directly manipulating next generation sequencing data in the cloud. Bioinformatics, 28(6):876-877, Feb. 2012.
29. L. Pireddu, S. Leo, and G. Zanetti. Mapreducing a genomic sequencing workflow. In Proceedings of the second international workshop on MapReduce and its applications, MapReduce '11, pages 67-74, New York, NY, USA, 2011. ACM.
30. A. R. Quinlan and I. M. Hall. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6):841-842, 2010.
31. P. Rice, I. Longden, and A. Bleasby. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet, 16(6):276-7, 2000.
32. T. Schairer, B. Huhle, P. Jenke, and W. Straber. Parallel Non-Local Denoising of Depth Maps. In International Workshop on Local and Non-Local Approximation in Image Processing (EUSIPCO Satellite Event), 2008.
33. M. C. Schatz. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics (Oxford, England), 25(11):1363-1369, 2009.
34. L. Stein. The case for cloud computing in genome informatics. Genome Biology, 11(5):207, 2010.
35. R. Taylor. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics, 11(Suppl 12):S1+, 2010.
36. Y. Wang, W. Jiang, and G. Agrawal. SciMATE: A Novel MapReduce-Like Framework for Multiple Scientific Data Formats. In Cluster, Cloud and Grid Computing (CCGrid), 2012 12th IEEE/ACM International Symposium on, pages 443-450. IEEE, 2012.
37. Y. Wang, Y. Su, and G. Agrawal. Supporting a light-weight data management layer over hdf5. In Cluster, Cloud and Grid Computing (CCGrid), 2013 13th IEEE/ACM International Symposium on, pages 335-342. IEEE, 2013.
38. J. Yang and Z. Fei. Broadcasting with prediction and selective forwarding in vehicular networks. International Journal of Distributed Sensor Networks, 2013, 2013.
39. B. Zhang, D. T. Yehdego, K. L. Johnson, M.-Y. Leung, and M. Taufer. Enhancement of accuracy and efficiency for rna secondary structure prediction by sequence segmentation and mapreduce. BMC Structural Biology, 13(Suppl 1):S3, 2013.