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Articles

Next-generation sequencing revolution through big data analytics

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Pages 119-149 | Received 17 Nov 2015, Accepted 11 Apr 2016, Published online: 10 May 2016

References

  • Aaron M, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20(9):1297–1303. doi: 10.1101/gr.107524.110
  • Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. 2012. Methylkit: a comprehensive R package for the analysis of genome-wide DNA methylation profile. Genome Biol. 13:R87. 10.1186/gb-2012-13-10-r87 doi: 10.1186/gb-2012-13-10-r87
  • Alexander NJ. 2014. On the middle ground between open source and commercial software – the case of the Newbler program. Genome Biol. 15(4):113. doi: 10.1186/gb4173
  • Ali M, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods. 5(7):621–628. doi: 10.1038/nmeth.1226
  • Amanda BJ, Bending GD, Chandler D, Hilton S, Mills P. 2012. Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations. Biol Rev. 87:52–71.
  • Ambros V. 2001. microRNAs: tiny regulators with great potential. Cell. 107:823–826. doi: 10.1016/S0092-8674(01)00616-X
  • Androniki P, Dovas CI, Bramis G, Lazou T, Russel CL, Arsenos G, Banos G. 2015. Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PLoS ONE. 10(1).
  • Bainbridge MN, Wang M, Wu Y, Newsham I, Muzny DM, Jefferies JL, Albert TJ, Burgess DL, Gibbs RA, Bainbridge, et al. 2011. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol. 12:R68. doi: 10.1186/gb-2011-12-7-r68
  • Bashir Y, Singh SP, Konwar BK. 2014. Metagenomics: an application based perspective. Chinese J Biol. 146030.7.
  • Bentley DR. 2004. Genomes for medicine. Nature. 429:440–445. 10.1038/nature02622 doi: 10.1038/nature02622
  • Brown SM. 2012. Sequencing-by-synthesis: explaining the illumina sequencing technology. Next Generation Sequencing.
  • Caboche S, Audebert C, Hot D. 2014. High-throughput sequencing, a versatile weapon to support genome-based diagnosis in infectious diseases: applications to clinical bacteriology. Pathog. 3(2):258–279. 10.3390/pathogens3020258 doi: 10.3390/pathogens3020258
  • Charlotte S, Delorenzi M. 2013. A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics. 14(1):91. doi: 10.1186/1471-2105-14-91
  • Chou H-C. 2012. Local assembly and pre-mRNA splicing analyses by high-throughput sequencing data. Graduate Theses and Dissertations. p. 12819.
  • Cole T, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat protoc. 7(3):562–578. doi: 10.1038/nprot.2012.016
  • Corney DC. 2013. RNA-seq using next generation sequencing. Mater Methods. 3:203. doi: 10.13070/mm.en.3.203
  • Costa FF. 2012. Big data in genomics: challenges and solutions. G.I.T. Laboratory Journal.
  • D’Antonio M, De Meo PD, Pallocca M, Picardi E, D’Erchia AM, Calogero RA, Castrignanò T, Pesole G. 2015. RAP: RNA-Seq analysis pipeline, a new cloud-based NGS web application. BMC Genomics. 16(6):S3. doi: 10.1186/1471-2164-16-S6-S3
  • David C, Chapman P, Trawley S, Collins L, Van Loon E, Andrews B, Underwood G. 2012. Some hazards are more attractive than others: drivers of varying experience respond differently to different types of hazard. Accident Anal Prev. 45:600–609. doi: 10.1016/j.aap.2011.09.049
  • Diroma MA, Calabrese C, Simone D, Santorsola M, Calabrese FM, Gasparre G, Attimonelli M. 2014. Extraction and annotation of human mitochondrial genomes from 1000 genomes whole exome sequencing data. BMC Genomics. 15(Suppl 3):S2. doi:10.1186/1471-2164-15-S3-S2
  • Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G. 2013. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc. 8:176–189. doi: 10.1038/nprot.2012.148
  • Doug H. 2012. Cloudera releases next-generation Hadoop platform. Information Week.
  • Elfving N, Razvan V, Bharatula CV, Bjorklund S, Morozov A, Broach J. 2014. A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress. Nucleic Acids Res. 10.1093/nar/gku176
  • Esmon CT. 2000. Regulation of blood coagulation. Biochim Bioph Acta. 1477(1–2):349–360. doi: 10.1016/S0167-4838(99)00266-6
  • Euskirchen GM, Rozowsky JS, Wei CL, Wah HL, Zhang ZD, Hartman S, Emanuelsson O. 2007. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 17(6):898–909. doi: 10.1101/gr.5583007
  • Fei Y. 2013. DNA sequencing, Sanger and next-generation sequencing. Singapore: Genome Institute of Singapore.
  • Feng X, Grossman R, Stein L. 2011. PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics. 12:139. doi:10.1186/1471-2105-12-139
  • Franca LTC, Carrilho E, Tarso B. 2002. A review of DNA sequencing techniques. Q Rev Biophys. 35(2):169–200. doi: 10.1017/S0033583502003797
  • Gaggero M, Leo S, Manca S, Santoni F, Schiaratura O, Zanetti G. 2008. Parallelizing bioinformatics applications with MapReduce. Cloud Computing and Its Application. 1–6.
  • Generation C. 2010. Illumina sequencing technology. Rochester, NY: Image. Vol. 21; p. 1–5.
  • Gianmauro C, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. 2014. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 30(13):1928–1929. doi: 10.1093/bioinformatics/btu135
  • Gonzaga-Jauregui C, Lupski JR, Gibbs RA. 2012. Human genome sequencing in health and disease. Annu Rev Med. 63(1):35–61. doi: 10.1146/annurev-med-051010-162644
  • Grada A, Weinbrecht K. 2013. Next-generation sequencing: methodology and application. J Invest Dermatol. 133:e11. doi:10.1038/jid.2013.248
  • Gregory CJ, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6(8):1621–1624. doi: 10.1038/ismej.2012.8
  • Großhans H, Friedrich Miescher Ins. 2010. Regulation of microRNAs, Landes Bioscience Espringer.
  • Guerreiro R, Bras J, Hardy J, Singleton A. 2014. Next generation sequencing techniques in neurological diseases: redefining clinical and molecular associations. Hum Mol Genet. doi:10.1093/hmg/ddu203
  • Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ. 2012. Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics. J Pathol Inform. 3:40. doi:10.4103/2153-3539.103013.
  • Gurtowski J, Schatz MC, Langmead B. 2012. Genotyping in the cloud with crossbow. Curr Protoc Bioinformatics. doi:10.1002/0471250953.bi1503s39
  • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB. 2013. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 8:1494–1512. doi:10.1038/nprot.2013.084
  • Head R, Steven R, Komori K, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. 2014. Library construction for next-generation sequencing: overviews and challenges. Biotechniques. 56(2):61–77.
  • Helga T, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Bioinform. 14(2):178–192.
  • Heng L, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 26(5):589–595. doi: 10.1093/bioinformatics/btp698
  • Heng L, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11):1851–1858. doi: 10.1101/gr.078212.108
  • Henk BPJ, Ariyurek Y, van Ommen G, den Dunnen JT, ‘t Hoen PAC. 2010. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 11:716. doi: 10.1186/1471-2164-11-716
  • Hong D, Rhie A, Park S-S, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, et al. 2012. FX: an RNA-seq analysis tool on the cloud. Bioinformatics. 28(5):721–733. doi: 10.1093/bioinformatics/bts023
  • Huang H, Pril TS. 2013. BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters. Bioinformatic. 29(1):135–136. doi: 10.1093/bioinformatics/bts647
  • Jared ST, Wong K, Jackman SD, Schein JE, Jones SJM. 2009. Inan?? Birol. ABySS: a parallel assembler for short read sequence data. Genome Res. 19(6):1117–1123. doi: 10.1101/gr.089532.108
  • Jarvie T, Harkins T. 2008. Transcriptome sequencing with the genome sequencer FLX system. Nat Methods (September). 5:6–8.
  • Jason Li, Maria AD, Isaam S, Stephen QW, Victoria M, David LG, Franco C, Ken D, Georgina LR, Ella RT, et al. 2014. Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human andmouse genomes: a virtual appliance approach for instant deployment. Plos ONE. doi:doi:10.1371/journal.pone.0095217
  • Jing S, Zhu F, Vongsangnak W, Tang Y, Zhang W, Shen B. 2014. Evaluation and comparison of multiple aligners for next-generation sequencing data analysis. BioMed Res Int.
  • John DW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 12(7):499–510. doi: 10.1038/nrg3012
  • John WC, Ye Y. 2009. Metagenomics: facts and artifacts, and computational challenges. J Comput Sci Tech. 25(1):71–81.
  • Jourdren L, Bernard M, Dillies M-A, Le Crom S. 2012. Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses. Bioinformatics. 28(11):1542–1543. doi: 10.1093/bioinformatics/bts165
  • Juliane DC, Lottaz C, Borodina T, Himmelbauer H. 2007. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17(11):1697–1706. doi: 10.1101/gr.6435207
  • Karchin R. 2009. Next generation tools for the annotation of human SNPs. Bioinform. 10:35–52.
  • Kelley DR, Schatz MC, Salzberg SL. 2010. Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 11:R116. doi:10.1186/gb-2010-11-11-r116
  • Kidder BL, Hu G, Zhao K. 2012. ChIP-Seq: technical considerations for obtaining high-quality data. Nat Immunol. 918–922. doi:10.1038/ni.2117
  • Koboldt DC, Zhang Q, Larson DE. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22:568–576. doi: 10.1101/gr.129684.111
  • Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz M. 2013. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Bio. 14:153–165. doi:10.1038/nrm3525
  • Lam KN, Hall MW, Engel K, Vey G, Cheng J, Neufeld JD, Charles TC. 2014. Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries. PloS ONE. doi:10.1371/journal.pone.0098968
  • Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. Plos ONE. 10.1371/journal.pone.0010071
  • Langmead B, Hansen KD, Leek JT. 2010. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 11(8):R83. doi:10.1186/gb-2010-11-8-r83
  • Leo S, Santoni F, Zanetti G. 2009. Biodoop: bioinformatics on Hadoop. Parallel processing workshops, 2009. ICPPW ‘09. International Conference on. doi:10.1109/ICPPW.2009.37
  • MacArthur D. 2009. Illumina launches personal genome sequencing service for $48,000. Scienceblogs.com.
  • MacFarlane L-A, Murphy PR. 2010. MicroRNA: biogenesis, function and role in cancer. Curr Genomics. 11(7):537–561. doi:10.2174/138920210793175895
  • Madhavan S. 2012. It’s not ‘just’ about BIGDATA – how to get to actionable clinical knowledge from BIGDATA. Innovation Center for Biomedical Informatics Georgetown University.
  • Mantha PK, Kim N, Lucknw A, Kim J, Jha S. 2012. Understanding mapreduce-based next-generation sequencing alignment on distributed cyberinfrastucture. ECMLS’12, ACM. 978-1-4503-1339-1/12/06.
  • Matsunaga A, Tsugawa M, Fortes J. 2008. CloudBLAST: combining MapReduce and virtualization on distributed resources for bioinformatics applications. EScience. 10.1109/eScience.2008.62
  • Matthias M, Stenzel U, Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nat protoc. 3(2):267–278. doi: 10.1038/nprot.2007.520
  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297–1303. doi: 10.1101/gr.107524.110
  • Meldrum C, Doyle MA, Tothill RW. 2011. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev. 32(4):177–195.
  • Metzker ML. 2010. Sequencing technologies – the next generation. Nat Rev Genet. 11:31–46. doi:10.1038/nrg2626
  • Mocellin S. 2007. Microarray technology and cancer gene profiling. Volume 593. ESpringer Science+Business Media, LLC Landes Bioscience/Eurekah.com.
  • Morozova O, Marra MA. 2008. Applications of next-generation sequencing technologies in functional genomics. Genomics. 92(5):255–264.
  • Mousumi D, Prasad GBKS, Bisen PS. 2005. Molecular diagnostics: promises and possibilities. Springer Netherlands; p. 1–520.
  • Nagalakshmi U, Waern K, Snyder M. 2010. RNA-Seq: a method for comprehensive transcriptome analysis. Curr Prot Mol Biol. doi:10.1002/0471142727.mb0411s89
  • Nextera Explain. Best Practices. 2013. Nextera DNA sample prep kit. Energy. 5(800):1–22.
  • Nguyen T, Shi W, Ruden D. 2011. CloudAligner: a fast and full-featured MapReduce based tool for sequence mapping. BMC Research Notes. 4:171. doi:10.1186/1756-0500-4-171
  • Niemenmaa M, Kallio A, Heljanko K. 2012. Hadoop-BAM: directly manipulating next generation sequencing data in the cloud. Bioinformatics. 28(6):876–877. doi: 10.1093/bioinformatics/bts054
  • NIH Nes Release publisher, National Institutes of Health. 2004. International human genome sequencing consortium describes finished human genome sequence.
  • O’Connor BD, Merriman B, Nelson SF. 2010. SeqWare query engine: storing and searching sequence data in the cloud. BMC Bioinformatics. doi:10.1186/1471-2105-11-S12-S2
  • O’Driscoll A, Daugelaiteb J, Sleatorb RD. 2013. ‘Big data’, Hadoop and cloud computing in genomics. J Biomed Inform. 46(5):774–781. doi:10.1016/j.jbi.2013.07.001
  • Pandey RV, Schlötterer C. 2013. DistMap: a toolkit for distributed short read mapping on a Hadoop cluster. Plos. doi:10.1371/journal.pone.0072614
  • Park PJ. 2009. ChIP-Seq: advantages and challenges of a maturing technology. Nat Rev Genet. 10(10):669–680. doi:10.1038/nrg2641
  • Patrice M. 2008. Helicos BIOSCIences. Pharmacogenomics. 9:477–480. doi: 10.2217/14622416.9.4.477
  • Paul TD. 2008. Single nucleotide polymorphisms in human disease and evolution: phylogenies and genealogies. Encycl Life Sci. 1–11. doi:doi:10.1002/9780470015902.a0020763.
  • Pireddu L, Leo S, Soranzo N. 2014. A Hadoop-galaxy adapter for user-friendly and scalable data-intensive bioinformatics in galaxy. ACM-BCB. doi:10.1145/2649387.264942
  • Pireddu L, Leo S, Zanetti G. 2011. SEAL: a distributed short read mapping and duplicate removal tool. Bioinformatics. 27(15):2159–2160. doi: 10.1093/bioinformatics/btr325
  • Pop M. 2009. Genome assembly reborn: recent computational challenges. Bioinform. 10(4):354–366. 10.1093/bib/bbp026
  • Pushkarev D, Neff N, Quake S. 2009. Single-molecule sequencing of an individual human genome. Nat Biotechnol. doi:10.1038/nbt.1561
  • Quail M, Miriam ES, Paul C, Thomas DO, Simon RH, Thomas RC, Anna B, Harold PS, Yong G. 2012. A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics. 13(1):p.1. doi:doi:10.1186/1471-2164-13-341
  • Quinlan A, Clark R, Hall I. 2010. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res. 20(5):623–635. doi: 10.1101/gr.102970.109
  • Raz T, Causey M, Jones DR, Kieu A, Letovsky S, Lipson D, Thayer E, Thompson JF, Milos PM. 2011. RNA-sequencing and quantitation using the helicos genetic analysis system. Methods Mol Biol. 733:37–49. 10.1007/978-1-61779-089-8_3 doi: 10.1007/978-1-61779-089-8_3
  • Renkema K, Stokman M, Giles R, Knoers N. 2014. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol. doi:10.1038/nrneph.95
  • Richar W, Blainey PC, Fan HC, Quake SR. 2009. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics. 10:116. doi: 10.1186/1471-2164-10-116
  • Roderic G, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S. 2006. EGASP: the human ENCODE genome annotation assessment project. Genome Biol. 7(1):1–31. doi: 10.1186/gb-2006-7-1-r1
  • Rong C, Davydov EV, Sirsota M, Butte AJ. 2010. Non-synonymous and synonymous coding SNPS show similar likelihood and effect size of human disease association. PLoS ONE. 5(10).
  • Schatz M, Delcher AL, Salzberga SL. 2010. Assembly of large genomes using second-generation sequencing. Genome Res. 20(9):1165–1173. doi: 10.1101/gr.101360.109
  • Schatz MC. 2009. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics. 25(11):1363–1369. doi: 10.1093/bioinformatics/btp236
  • Schumacher A, Pireddu L, Niemenmaa M, Kallio A, Korpelainen E, Zanetti G, Heljanko K. 2014. SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. Bioinformatics. 30(1):119–120. doi: 10.1093/bioinformatics/btt601
  • Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol. 26(10):1135–1145. doi: 10.1038/nbt1486
  • Shivakumar SK. 2013. Big Data – a big game changer. CSI Communications.
  • Sol-Church K, Catalano S, Holbrook J, Stabley D, Conard K. 2009. SR1-S1 HRAS Mutations and 11p allelic imbalance in a rare case of agminated spitz nevus: bridging the gap between bench and bedside through collaborative research. J Biomol Tech. 20(1):31–89.
  • Srivatsan A, Han Y, equal contributor, Peng J, Tehranchi A, Gibbs R, Wang J, Chen R. 2008. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PloS Genetics. doi:10.1371/journal.pgen.1000139
  • Stephen RM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. 5(5).
  • Stephen GL, Georgi KM, Anshul K, Pouya K, Florencia P, Serafim B, Bradley EB, Peter B, James BB, Philip C, et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome. 22(9):1813–1831. doi: 10.1101/gr.136184.111
  • Strachan T, Read AP. 1999. Identifying human disease genes. In: Human Molecular Genetics. 2nd ed. Chapter 15.
  • Tanja M, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27(21):2957–2963. doi: 10.1093/bioinformatics/btr507
  • Taylor RC. 2010. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics. 11(Suppl 12):S1. 10.1186/1471-2105-11-S12-S1 doi: 10.1186/1471-2105-11-S12-S1
  • Thamizhvanan R, Himabindu KS, Hyndavi N, Roopa LK. 2012. The human genome project. Int J Phar Rev Res. 2(1):31–45.
  • Thomas T, Gilbert J, Meyer F. 2012. Metagenomics – a guide from sampling to data analysis. Microb Inform Exper. 2:3. doi:10.1186/2042-5783-2-3
  • Totty M. 2005. A better idea. The Wall Street Journal.
  • Trapnell C, Salzberg SL. 2010. How to map billions of short reads onto genomes. Nat Biotechnol. 27(5):455–457. doi:10.1038/nbt0509-455
  • Turan N, Ghalwash MF, Katari S, Coutifaris C, Obradovic Z, Sapienz C. 2012. DNA methylation differences at growth related genes correlate with birth weight: a molecular signature linked to developmental origins of adult disease? BMC Med Genomics. 5:10. 10.1186/1755-8794-5-10 doi: 10.1186/1755-8794-5-10
  • Van Neste C, Gansemans Y, De Coninck D, Van Hoofstat D, Van Criekinge W, Deforce D, Van Nieuwerburgh F. 2015. Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace??-application. Forensic Sci Int: Genetics. 15:2–7. doi: 10.1016/j.fsigen.2014.10.006
  • Velikkakam JG, Patel V, Nordström KJV, Klasen JR, Salomé PA, Weigel D, Schneeberger K. 2013. User guide for mapping-by-sequencing in arabidopsis. Genome Biol. 14:6–61. doi: 10.1186/gb-2013-14-1-r6
  • Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP. 2011. A low-cost library construction protocol and data analysis pipeline for illumina-based strand-specific multiplex RNA-Seq. PloS ONE. doi:10.1371/journal.pone.0026426
  • Warren LR, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4):500–501. doi: 10.1093/bioinformatics/btl629
  • Watson JD. 1990. The human genome project: past, present, and future. Science. 248:44–49. doi: 10.1126/science.2181665
  • White T. 2010. Hadoop: the definitive guide. O’Reilly Media/Yahoo Press.
  • Xianwen R, Liu T, Dong J, Sun L, Yang J, Zhu Y, Jin Q. 2012. Evaluating de Bruijn graph assemblers on 454 transcriptomic data. PLoS ONE. 7(12).
  • Ye J, Renault VM, Jamet K, Gilson E. 2014. Transcriptional outcome of telomere signalling. Nat Rev Genet. 10,15(7):491–503. doi: 10.1038/nrg3743
  • Yuichi K, Shumway M, Leinonen R. 2012. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res. 40.D1.
  • Zerbino R, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5):821–829. doi: 10.1101/gr.074492.107

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