Rainbow: A tool for large-scale whole-genome sequencing data analysis using cloud computing

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Zhao, Shanrong ^a   Prenger, Kurt ^b   Smith, Lance ^a   Messina, Thomas ^b   Fan, Hongtao ^a   Jaeger, Edward ^a   Stephens, Susan ^a  

^a JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

^b JOHNSON AND JOHNSON   (United States)

Author keywords

Cloud computing; Next generation sequencing; Single nucleotide polymorphism; SNP; Software; Whole genome sequencing

Indexed keywords

ARTICLE; AUTOMATION; CLOUD COMPUTING; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; COST; DATA ANALYSIS; DATA PROCESSING; GENE SEQUENCE; GENETIC ASSOCIATION; GENOMICS; INFORMATION PROCESSING; SAMPLE; TIME;

CLUSTER ANALYSIS; GENOMICS; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS; SOFTWARE; STATISTICS AS TOPIC;

EID: 84879425374     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-425     Document Type: Article

References (33)

1. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59. 10.1038/nature07517, 2581791,2581791, 18987734.
2. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009, 19:1527-1541. 10.1101/gr.091868.109, 2752135, 19546169.
3. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, et al. The diploid genome sequence of an Asian individual. Nature 2008, 456:60-65. 10.1038/nature07484, 2716080, 18987735.
4. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
5. Baker M. Next-generation sequencing: adjusting to data overload. Nat Methods 2010, 7:495-499.
6. Schatz M, Langmead B, Salzberg SL. Cloud computing and the DNA data race. Nat Biotechnol 2010, 28:691-693. 10.1038/nbt0710-691, 2904649, 20622843.
7. Stein LD. The case for cloud computing in genome informatics. Genome Biol 2010, 11:207. 10.1186/gb-2010-11-5-207, 2898083, 20441614.
8. Shanker A. Genome research in the cloud. OMICS. 2012, 16:422-428. 10.1089/omi.2012.0001, 22734722.
9. Angiuoli SV, White JR, Matalka M, White O, Fricke WF. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS One 2011, 6:e26624. 10.1371/journal.pone.0026624, 3197577, 22028928.
10. Cloud computing tools and analyses [http://genomebiology.com/series/cloudcomputing].
11. Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009, 25:1363-1369. 10.1093/bioinformatics/btp236, 2682523, 19357099.
12. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Genotyping in the cloud with Crossbow. Curr Protoc Bioinformatics 2012, 15. Unit15.3.
13. Gurtowski J, Schatz MC, Langmead B. Genotyping in the cloud with crossbow. Genome Biol 2009, 10:R134. 10.1186/gb-2009-10-11-r134, 3091327, 19930550.
14. Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol 2010, 11:R83. 10.1186/gb-2010-11-8-r83, 2945785, 20701754.
15. Angiuoli SV, Matalka M, Gussman G, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011, 12:356. 10.1186/1471-2105-12-356, 3228541, 21878105.
16. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
17. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714. 10.1093/bioinformatics/btn025, 18227114.
18. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
19. Welcome to Apache Hadoop! [http://hadoop.apache.org/].
20. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K. SNP detection for massively parallel whole-genome resequencing. Genome Res 2009, 19:1124-1132. 10.1101/gr.088013.108, 2694485, 19420381.
21. Amazon Simple Storage Service (Amazon S3) [http://aws.amazon.com/s3/].
22. Amazon Elastic Compute Cloud (Amazon EC2) [http://aws.amazon.com/ec2/].
23. Command line S3 client [http://s3tools.org/s3cmd].
24. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet. 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
25. Picard [http://picard.sourceforge.net/].
26. S3Fox [http://www.s3fox.net/].
27. CloudInit [https://help.ubuntu.com/community/CloudInit].
28. Elastic Block Storage [http://aws.amazon.com/ebs/].
29. Boto [http://docs.pythonboto.org/en/latest/index.html].
30. HDFS [http://hadoop.apache.org/docs/hdfs/current/hdfs_design.html].
31. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zöllner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 2012, 337:100-104. 10.1126/science.1217876, 22604722.
32. Tran B, Brown AM, Bedard PL, Winquist E, Goss GD, Hotte SJ, Welch SA, Hirte HW, Zhang T, Stein LD, Ferretti V, Watt S, Jiao W, Ng K, Ghai S, Shaw P, Petrocelli T, Hudson TJ, Neel BG, Onetto N, Siu LL, McPherson JD, Kamel-Reid S, Dancey JE. Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial. Int J Cancer 2013, 132:1547. 1555, 10.1002/ijc.27817, 22948899.
33. Rainbow website [http://s3.amazonaws.com/jnj_rainbow/index.html].