High-performance integrated virtual environment (hive) tools and applications for big data analysis

Genes

Volumn 5, Issue 4, 2014, Pages 957-981

  Simonyan, Vahan ^a   Mazumder, Raja ^b  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^b GEORGE WASHINGTON UNIVERSITY SCHOOL OF MEDICINE AND HEALTH SCIENCES   (United States)

Author keywords

Big data; Bioinformatics; Genomics; High performance cloud computing; High throughput sequencing; Next generation sequencing

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER ANALYSIS; COMPUTER PROGRAM; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA BASE; GENE SEQUENCE; GENETIC ANALYZER; HIGH PERFORMANCE INTEGRATED VIRTUAL ENVIRONMENT; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; INFORMATION CENTER; INFORMATION PROCESSING; METAGENOMICS; NEXT GENERATION SEQUENCING; PHYLOGENY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; WORKFLOW;

EID: 84919668205     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes5040957     Document Type: Article

References (88)

1. Metzker, M.L. Sequencing technologies—The next generation. Nat. Rev. Genet. 2010, 11, 31-46.
2. Yadav, N.K.; Shukla, P.; Omer, A.; Pareek, S.; Singh, R.K. Next generation sequencing: Potential and application in drug discovery. Sci. World J. 2014, 2014, e802437.
3. Mardis, E.R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 2008, 9, 387-402.
4. Dolled-Filhart, M.P.; Lee, M., Jr.; Ou-Yang, C.W.; Haraksingh, R.R.; Lin, J.C. Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. Sci. World J. 2013, 2013, e730210.
5. Pop, M.; Salzberg, S.L. Bioinformatics challenges of new sequencing technology. Trends Genet. 2008, 24, 142-149.
6. Marx, V. Biology: The big challenges of big data. Nature 2013, 498, 255-260.
7. Mardis, E.R. A decade’s perspective on DNA sequencing technology. Nature 2011, 470, 198-203.
8. HIVE. Available online: https://hive.biochemistry.gwu.edu??(accessed on 24 September 2014).
9. Liolios, K.; Tavernarakis, N.; Hugenholtz, P.; Kyrpides, N.C. The genomes on line database (gold) v.2: A monitor of genome projects worldwide. Nucleic Acids Res. 2006, 34, D332-D334.
10. Chen, J.; Qian, F.; Yan, W.; Shen, B. Translational biomedical informatics in the cloud: Present and future. BioMed Res. Int. 2013, 2013, e658925.
11. Treangen, T.J.; Salzberg, S.L. Repetitive DNA and next-generation sequencing: Computational challenges and solutions. Nat. Rev. Genet. 2012, 13, 36-46.
12. Pop, M. Genome assembly reborn: Recent computational challenges. Brief. Bioinform. 2009, 10, 354-366.
13. Simon, R.; Roychowdhury, S. Implementing personalized cancer genomics in clinical trials. Nat. Rev. Drug Discovery 2013, 12, 358-369.
14. Brown, J.; Ahamad, M.; Ahmed, M.; Blough, D.M.; Kurc, T.; Post, A.; Saltz, J. Redactable and auditable data access for bioinformatics research. In Proceedings of AMIA Joint Summits on Translational Science, San Francisco, CA, USA, 18-22 March 2013; pp. 21-25.
15. Roos, D.S. Computational biology. Bioinformatics trying to swim in a sea of data. Science 2001, 291, 1260-1261.
16. Tao, Y.; Liu, Y.; Friedman, C.; Lussier, Y.A. Information visualization techniques in bioinformatics during the postgenomic era. Drug Discov. Today 2004, 2, 237-245.
17. Loraine, A.E.; Helt, G.A. Visualizing the genome: Techniques for presenting human genome data and annotations. BMC Bioinform. 2002, 3, e19.
18. Wu, T.J.; Shamsaddini, A.; Pan, Y.; Smith, K.; Crichton, D.J.; Simonyan, V.; Mazumder, R. A framework for organizing cancer-related variations from existing databases, publications and ngs data using a high-performance integrated virtual environment (HIVE). Database (Oxford) 2014, 2014, bau022.
19. Karagiannis, K.; Simonyan, V.; Mazumder, R. Snvdis: A proteome-wide analysis service for evaluating nssnvs in protein functional sites and pathways. Genom. Proteom. Bioinform. 2013, 11, 122-126.
20. Cole, C.; Krampis, K.; Karagiannis, K.; Almeida, J.S.; Faison, W.J.; Motwani, M.; Wan, Q.; Golikov, A.; Pan, Y.; Simonyan, V., et al. Non-synonymous variations in cancer and their effects on the human proteome: Workflow for ngs data biocuration and proteome-wide analysis of TCGA data. BMC Bioinform. 2014, 15, e28.
21. Abunimer, A.; Smith, K.; Wu, T.J.; Lam, P.; Simonyan, V.; Mazumder, R. Single-nucleotide variations in cardiac arrhythmias: Prospects for genomics and proteomics based biomarker discovery and diagnostics. Genes 2014, 5, 254-269.
22. Wooley, J.C.; Godzik, A.; Friedberg, I. A primer on metagenomics. PLoS Comput. Biol. 2010, 6, e1000667.
23. Francis, O.E.; Bendall, M.; Manimaran, S.; Hong, C.; Clement, N.L.; Castro-Nallar, E.; Snell, Q.; Schaalje, G.B.; Clement, M.J.; Crandall, K.A., et al. Pathoscope: Species identification and strain attribution with unassembled sequencing data. Genome Res. 2013, 23, 1721-1729.
24. Liu, B.; Gibbons, T.; Ghodsi, M.; Treangen, T.; Pop, M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 2011, 12 Suppl 2, S4.
25. Gaudet, P.; Arighi, C.; Bastian, F.; Bateman, A.; Blake, J.A.; Cherry, M.J.; D'Eustachio, P.; Finn, R.; Giglio, M.; Hirschman, L., et al. Recent advances in biocuration: Meeting report from the fifth international biocuration conference. Database (Oxford) 2012, 2012, bas036.
26. Segata, N.; Waldron, L.; Ballarini, A.; Narasimhan, V.; Jousson, O.; Huttenhower, C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 2012, 9, 811-814.
27. McGinnis, S.; Madden, T.L. Blast: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 2004, 32, W20-W25.
28. Chen, C.; Natale, D.A.; Finn, R.D.; Huang, H.; Zhang, J.; Wu, C.H.; Mazumder, R. Representative proteomes: A stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS ONE 2011, 6, e18910.
29. Hatem, A.; Bozdag, D.; Toland, A.E.; Catalyurek, U.V. Benchmarking short sequence mapping tools. BMC Bioinform. 2013, 14, e184.
30. Ruffalo, M.; LaFramboise, T.; Koyuturk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011, 27, 2790-2796.
31. Santana-Quintero, L.; Dingerdissen, H.; Thierry-Mieg, J.; Mazumder, R.; Simonyan, V. Hive-hexagon: High-performance, parallelized sequence alignment for next-generation sequencing data analysis. PLoS ONE 2014, 9, e99033.
32. DePristo, M.A.; Banks, E.; Poplin, R.; Garimella, K.V.; Maguire, J.R.; Hartl, C.; Philippakis, A.A.; del Angel, G.; Rivas, M.A.; Hanna, M., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011, 43, 491-498.
33. Meldrum, C.; Doyle, M.A.; Tothill, R.W. Next-generation sequencing for cancer diagnostics: A practical perspective. Clin. Biochem. Rev. 2011, 32, 177-195.
34. Faison, W.J.; Rostovtsev, A.; Castro-Nallar, E.; Crandall, K.A.; Chumakov, K.; Simonyan, V.; Mazumder, R. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Genomics 2014, 104, 1-7.
35. Van Geystelen, A.; Decorte, R.; Larmuseau, M.H. Amy-tree: An algorithm to use whole genome snp calling for y chromosomal phylogenetic applications. BMC Genomics 2013, 14, e101.
36. Leekitcharoenphon, P.; Kaas, R.S.; Thomsen, M.C.; Friis, C.; Rasmussen, S.; Aarestrup, F.M. Snptree—A web-server to identify and construct snp trees from whole genome sequence data. BMC Genomics 2012, 13 (Suppl 7), S6.
37. Forbes, S.A.; Bindal, N.; Bamford, S.; Cole, C.; Kok, C.Y.; Beare, D.; Jia, M.; Shepherd, R.; Leung, K.; Menzies, A., et al. Cosmic: Mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2011, 39, D945-D950.
38. Clin Var. Available online: http://www.ncbi.nlm.nih.gov/clinvar??(accessed on 15 August 2014).
39. UniProt Consortium. Activities at the universal protein resource (uniprot). Nucleic Acids Res. 2014, 42, D191-D198.
40. Sayers, E.W.; Barrett, T.; Benson, D.A.; Bolton, E.; Bryant, S.H.; Canese, K.; Chetvernin, V.; Church, D.M.; Dicuccio, M.; Federhen, S., et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2010, 38, D5-D16.
41. Punta, M.; Coggill, P.C.; Eberhardt, R.Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J., et al. The pfam protein families database. Nucleic Acids Res. 2012, 40, D290-D301.
42. Pruitt, K.D.; Tatusova, T.; Brown, G.R.; Maglott, D.R. NCBI reference sequences (refseq): Current status, new features and genome annotation policy. Nucleic Acids Res. 2012, 40, D130-D135.
43. Marchler-Bauer, A.; Zheng, C.; Chitsaz, F.; Derbyshire, M.K.; Geer, L.Y.; Geer, R.C.; Gonzales, N.R.; Gwadz, M.; Hurwitz, D.I.; Lanczycki, C.J., et al. Cdd: Conserved domains and protein three-dimensional structure. Nucleic Acids Res. 2013, 41, D348-D352.
44. Mi, H.; Lazareva-Ulitsky, B.; Loo, R.; Kejariwal, A.; Vandergriff, J.; Rabkin, S.; Guo, N.; Muruganujan, A.; Doremieux, O.; Campbell, M.J., et al. The panther database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005, 33, D284-D288.
45. Howe, D.; Costanzo, M.; Fey, P.; Gojobori, T.; Hannick, L.; Hide, W.; Hill, D.P.; Kania, R.; Schaeffer, M.; St Pierre, S., et al. Big data: The future of biocuration. Nature 2008, 455, 47-50.
46. NCI Cancer Genomics Program. Available online: http://cancergenome.nih.gov???(accessed on 15 August 2014).
47. The Cancer Genome Atlas (TCGA). Available online: http://cancergenome.nih.gov???(accessed on 15 August 2014).
48. Cancer Genomics Hub (CGHub). Available online: https://cghub.ucsc.edu (accessed on 15 August 2014).
49. Kodama, Y.; Shumway, M.; Leinonen, R. The sequence read archive: Explosive growth of sequencing data. Nucleic Acids Res. 2012, 40, D54-D56.
50. Lauring, A.S.; Andino, R. Quasispecies theory and the behavior of rna viruses. PLoS Pathog. 2010, 6, e1001005.
51. Domingo, E. Rapid evolution of viral RNA genomes. J. Nutr. 1997, 127, 958S-961S.
52. Li, H.; Durbin, R. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics 2010, 26, 589-595.
53. Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9, 357-359.
54. Kent, W.J. Blat—The blast-like alignment tool. Genome Res. 2002, 12, 656-664.
55. Larkin, M.A.; Blackshields, G.; Brown, N.P.; Chenna, R.; McGettigan, P.A.; McWilliam, H.; Valentin, F.; Wallace, I.M.; Wilm, A.; Lopez, R., et al. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23, 2947-2948.
56. Katoh, K.; Misawa, K.; Kuma, K.; Miyata, T. Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 2002, 30, 3059-3066.
57. Zerbino, D.R.; Birney, E. Velvet: Algorithms for de novo short read assembly using de bruijn graphs. Genome Res. 2008, 18, 821-829.
58. Simpson, J.T.; Wong, K.; Jackman, S.D.; Schein, J.E.; Jones, S.J.; Birol, I. Abyss: A parallel assembler for short read sequence data. Genome Res. 2009, 19, 1117-1123.
59. Trapnell, C.; Pachter, L.; Salzberg, S.L. Tophat: Discovering splice junctions with RNA-seq. Bioinformatics 2009, 25, 1105-1111.
60. Zhu, W.; Lomsadze, A.; Borodovsky, M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010, 38, e132.
61. Besemer, J.; Borodovsky, M. Genemark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005, 33, W451-W454.
62. Pedruzzi, I.; Rivoire, C.; Auchincloss, A.H.; Coudert, E.; Keller, G.; de Castro, E.; Baratin, D.; Cuche, B.A.; Bougueleret, L.; Poux, S., et al. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 2013, 41, D584-D589.
63. Poux, S.; Magrane, M.; Arighi, C.N.; Bridge, A.; O'Donovan, C.; Laiho, K. Expert curation in uniprotkb: A case study on dealing with conflicting and erroneous data. Database (Oxford) 2014, 2014, bau016.
64. Amazon Web Services (AWS). Available online: http://aws.amazon.com??(accessed on 30 August 2014).
65. Rackspace. Available online: http://www.rackspace.com??(accessed on 30 August 2014).
66. Flexiant. Available online: http://www.flexiant.com??(accessed on 30 August 2014).
67. Google Cloud. Available online: https://cloud.google.com??(accessed on 30 August 2014).
68. Stein, L.D. The case for cloud computing in genome informatics. Genome Biol. 2010, 11, e207.
69. Fusaro, V.A.; Patil, P.; Gafni, E.; Wall, D.P.; Tonellato, P.J. Biomedical cloud computing with amazon web services. PLoS Comput. Biol. 2011, 7, e1002147.
70. El-Kalioby, M.; Abouelhoda, M.; Kruger, J.; Giegerich, R.; Sczyrba, A.; Wall, D.P.; Tonellato, P. Personalized cloud-based bioinformatics services for research and education: Use cases and the elastichpc package. BMC Bioinform. 2012, 13 (Suppl 17), S22.
71. Krampis, K.; Booth, T.; Chapman, B.; Tiwari, B.; Bicak, M.; Field, D.; Nelson, K.E. Cloud biolinux: Pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinform. 2012, 13, e42.
72. Romano, P. Automation of in-silico data analysis processes through workflow management systems. Brief. Bioinform. 2008, 9, 57-68.
73. Wolstencroft, K.; Haines, R.; Fellows, D.; Williams, A.; Withers, D.; Owen, S.; Soiland-Reyes, S.; Dunlop, I.; Nenadic, A.; Fisher, P., et al. The taverna workflow suite: Designing and executing workflows of web services on the desktop, web or in the cloud. Nucleic Acids Res. 2013, 41, W557-W561.
74. Goecks, J.; Nekrutenko, A.; Taylor, J. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11, R86.
75. Orvis, J.; Crabtree, J.; Galens, K.; Gussman, A.; Inman, J.M.; Lee, E.; Nampally, S.; Riley, D.; Sundaram, J.P.; Felix, V., et al. Ergatis: A web interface and scalable software system for bioinformatics workflows. Bioinformatics 2010, 26, 1488-1492.
76. Romano, P.; Bartocci, E.; Bertolini, G.; de Paoli, F.; Marra, D.; Mauri, G.; Merelli, E.; Milanesi, L. Biowep: A workflow enactment portal for bioinformatics applications. BMC Bioinform. 2007, 8 (Suppl 1), S19.
77. Garcia Castro, A.; Thoraval, S.; Garcia, L.J.; Ragan, M.A. Workflows in bioinformatics: Meta-analysis and prototype implementation of a workflow generator. BMC Bioinform. 2005, 6, e87.
78. Linke, B.; Giegerich, R.; Goesmann, A. Conveyor: A workflow engine for bioinformatic analyses. Bioinformatics 2011, 27, 903-911.
79. Pegasus. Available online: http://pegasus.isi.edu??(accessed on 30 August 2014).
80. Tang, F.; Chua, C.L.; Ho, L.Y.; Lim, Y.P.; Issac, P.; Krishnan, A. Wildfire: Distributed, grid-enabled workflow construction and execution. BMC Bioinform. 2005, 6, e69.
81. Kepler. Available online: https://kepler-project.org??(accessed on 30 August 2014).
82. Blankenberg, D.; von Kuster, G.; Coraor, N.; Ananda, G.; Lazarus, R.; Mangan, M.; Nekrutenko, A.; Taylor, J. Galaxy: A web-based genome analysis tool for experimentalists. In Current Protocols in Molecular Biology; Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., Struhl, K., Eds.; John Wiley & Sons: New York, USA 2010; Chapter 19, pp. 11-21.
83. Galaxy Wiki. Available online: https://wiki.galaxyproject.org/CloudMan?action=show&redirect= Admin%2FCloud (accessed on 30 August 2014).
84. CLC Bio. Available online: http://www.clcbio.com??(accessed on 30 August 2014).
85. Seven Bridges. Available online: https://www.sbgenomics.com??(accessed on 30 August 2014).
86. Seven Bridges taps Bioteam to develop cloud-enabled appliance for NGS. Available online: https://www.sbgenomics.com?/press/bioteam?(accessed on 30 August 2014).
87. DNAnexus. Available online: https://dnanexus.com??(accessed on 30 August 2014).
88. Lampa, S.; Dahlo, M.; Olason, P.I.; Hagberg, J.; Spjuth, O. Lessons learned from implementing a national infrastructure in sweden for storage and analysis of next-generation sequencing data. GigaScience 2013, 2, e9.