Электронный журнал | Том 11 Выпуск 2 Год 2016

Аулов В.А., Климентов А.А., Машинистов Р.Ю., Недолужко А.В., Новиков А.М., Пойда А.А., Тертычный И.С., Теслюк А.Б., Шарко Ф.С.

Интеграция гетерогенных вычислительных инфраструктур для анализа данных геномного секвенирования

Математическая биология и биоинформатика. 2016;11(2):205-213.

doi: 10.17537/2016.11.205.

Список литературы

Skryabin K.G., Prokhortchouk E.B., Mazur A.M., Boulygina E.S., Tsygankova S.V., Nedoluzhko A.V., Rastorguev S.M., Matveev V.B., Chekanov N.N., Goranskaya D.A., Teslyuk A.B., Gruzdeva N.M., Velikhov V.E., Zaridze D.G., Kovalchuk M.V. Combining two technologies for full genome sequencing of human. Acta Nat. 2009;1(3):102-107.
Kawalia A., Motameny S., Wonczak S., Thiele H., Nieroda L., Jabbari K., Borowski S., Sinha V., Gunia W., Lang U., Achter V., Nurnberg P. Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow. PLoS One. 2015;10(5). Article No e0126321. doi: 10.1371/journal.pone.0126321
Bao R., Huang L., Andrade J., Tan W., Kibbe W.A., Jiang H., Feng G. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Inform. 2014;13(2):67-82.
Miller W., Drautz D.I., Ratan A., Pusey B., Qi J., Lesk A.M., Tomsho L.P., Packard M.D., Zhao F., Sher A., Tikhonov A., Raney B., Patterson N., Linblad-Toh K., Lander E.S., Knight J.R., Irzyk G.P. Fredrikson K.M., Harkins T.T., Sheridan S., Pringle T., Schuster S.C. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008;456:387-390. doi: 10.1038/nature07446
Rasmussen M., Li Y., Lindgreen S., Pedersen J.S., Albrechtsen A., Moltke I., Metspalu M., Metspalu E., Kivisild T., Gupta R., et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2009;463:757-762. doi: 10.1038/nature08835
Keller A., Graefen A., Ball M., Matzas M., Boisguerin V., Maixner F., Leidinger P., Backes C., Khairat R., Forster M., et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature Communications. 2011;3.
Allentoft M.E., Collins M., Harker D., Haile J., Oskam C.L., Hale M.L., Campos P.F., Samaniego J.A., Gilbert M.T., Willerslev E., et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci. 2012;279:4724-4733. doi: 10.1098/rspb.2012.1745
Nedoluzhko A.V., Boulygina E.S., Sokolov A.S., Tsygankova S.V., Gruzdeva N.M., Rezepkin A.D., Prokhortchouk E.B. Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture. Acta Naturae. 2014;6:31-35.
Sokolov A.S., Nedoluzhko A.V., Boulygina E.S., Tsygankova S.V., Gruzdeva N.M., Shishlov A.V., Kolpakova A., Rezepkin A.D., Skryabin K.G., Prokhortchouk E.B. Six complete mitochondrial genomes from Early Bronze Age humans in the North Caucasus. Journal of Archaeological Sciences. 2016;73:138-144. doi: 10.1016/j.jas.2016.07.017
Martin M.D., Cappellini E., Samaniego J.A., Zepeda M.L., Campos P.F., Seguin-Orlando A., Wales N., Orlando L., Ho S.Y., Dietrich F.S., et al. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications. 2013;4. doi: 10.1038/ncomms3172
Yoshida K., Schuenemann V.J., Cano L.M., Pais M., Mishra B., Sharma R., Lanz C., Martin F.N., Kamoun S., Krause J., et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife. 2013;2.
Lorenzen E.D., Nogues-Bravo D., Orlando L., Weinstock J., Binladen J., Marske K.A., Ugan A., Borregaard M.K., Gilbert M.T., Nielsen R., et al. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature. 2011;479:359-364. doi: 10.1038/nature10574
Lynch V.J., Bedoya-Reina O.C., Ratan A., Sulak M., Drautz-Moses D.I., Perry G.H., Miller W., Schuster S.C. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Сell Rep. 2015;12(2):217-228. doi: 10.1016/j.celrep.2015.06.027
Massie M., Nothaft F., Hartl C., Kozanitis C., Schumacher A., Joseph A.D., Patterson D.A. ADAM: genomics formats and processing patterns for cloud scale computing: Report No.: UCB/EECS-2013-207. Berkeley: EECS Department, University of California, Berkeley; 2013.
Schubert M., Ermini L., Sarkissian C.D., Jonsson H., Ginolhac A., Schaefer R., Martin M.D., Fernandez R., Kircher M., McCue M., Willerslev E., Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc. 2014;9:1056-1082. doi: 10.1038/nprot.2014.063
The ATLAS Collaboration, G Aad et al., The ATLAS Experiment at the CERN Large Hadron Collider. Journal of Instrumentation. 2008;3. http://iopscience.iop.org/article/10 (accessed 28 September 2016).
The Large Hadron Collider. http://home.cern/topics/large-hadron-collider (accessed 28 September 2016).
Maeno T. on behalf of PANDA team and ATLAS collaboration. PanDA: distributed production and distributed analysis system for ATLAS. Journal of Physics: Conference Series. 2008;119(6). doi: 10.1088/1742-6596/119/6/062036
Maeno T., De K., Klimentov A., Nilsson P., Oleynik D., Panitkin S., Petrosyan A., Schovancova J., Vaniachine A., Wenaus T. Evolution of the ATLAS PanDA workload management system for exascale computational science. J. Phys.: Conf. Ser. 2014;513. doi: 10.1088/1742-6596/513/3/032062
Worldwide LHC Computing Grid. http://wlcg.web.cern.ch/ (accessed 28 September 2016).