The ENCODE Uniform Analysis Pipelines.
| العنوان: | The ENCODE Uniform Analysis Pipelines. |
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| المؤلفون: | Hitz BC; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Lee JW; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Jolanki O; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Kagda MS; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Graham K; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Sud P; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Gabdank I; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Strattan JS; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Sloan CA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Dreszer T; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Rowe LD; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Podduturi NR; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Malladi VS; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Chan ET; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Davidson JM; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Ho M; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Miyasato S; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Simison M; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Tanaka F; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Luo Y; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Whaling I; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Hong EL; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA., Lee BT; Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Sandstrom R; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Rynes E; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Nelson J; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Nishida A; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Ingersoll A; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Buckley M; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Frerker M; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA., Kim DS; Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA., Boley N; Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA., Trout D; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA., Dobin A; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA., Rahmanian S; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA., Wyman D; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA., Balderrama-Gutierrez G; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA., Reese F; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA., Durand NC; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.; Department of Computer Science, Rice University, Houston, TX 77030, USA., Dudchenko O; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Weisz D; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Rao SSP; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA., Blackburn A; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA., Gkountaroulis D; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA., Sadr M; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Olshansky M; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Eliaz Y; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Nguyen D; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Bochkov I; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Shamim MS; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.; Department of Bioengineering, Rice University, Houston, TX 77030, USA.; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA., Mahajan R; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.; Department of BioSciences, Rice University, Houston, TX 77005, USA., Aiden E; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA., Gingeras T; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA., Heath S; CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain., Hirst M; Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada., Kent WJ; Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Kundaje A; Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA., Mortazavi A; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA., Wold B; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA., Cherry JM; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. |
| المصدر: | Research square [Res Sq] 2023 Jul 19. Date of Electronic Publication: 2023 Jul 19. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101768035 Publication Model: Electronic Cited Medium: Internet ISSN: 2693-5015 (Electronic) Linking ISSN: 26935015 NLM ISO Abbreviation: Res Sq Subsets: PubMed not MEDLINE |
| مستخلص: | The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses. Competing Interests: Conflict of interest. None declared |
| References: | Science. 2021 May 28;372(6545):984-989. (PMID: 34045355) Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. (PMID: 27079975) Nat Biotechnol. 2016 May;34(5):525-7. (PMID: 27043002) Curr Protoc Mol Biol. 2013 Jul;Chapter 27:Unit 21.27. (PMID: 23821440) Curr Protoc Bioinformatics. 2019 Dec;68(1):e89. (PMID: 31751002) BMC Bioinformatics. 2011 Aug 04;12:323. (PMID: 21816040) Nat Methods. 2012 Mar 04;9(4):357-9. (PMID: 22388286) Genome Res. 2013 Jan;23(1):169-80. (PMID: 22936248) PLoS One. 2017 Apr 12;12(4):e0175310. (PMID: 28403240) Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278) Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168) Nat Biotechnol. 2014 Apr;32(4):341-6. (PMID: 24633242) Nat Biotechnol. 2010 Oct;28(10):1045-8. (PMID: 20944595) Nucleic Acids Res. 2023 Jan 6;51(D1):D1188-D1195. (PMID: 36420891) Bioinformatics. 2010 Sep 1;26(17):2204-7. (PMID: 20639541) Bioinformatics. 2019 Mar 1;35(5):737-742. (PMID: 30137223) Nature. 2017 Sep 13;549(7671):219-226. (PMID: 28905911) Nat Methods. 2014 Jan;11(1):41-6. (PMID: 24141493) Cell. 2014 Dec 18;159(7):1665-80. (PMID: 25497547) Cell Syst. 2016 Jul;3(1):95-8. (PMID: 27467249) Cell Syst. 2018 Feb 28;6(2):256-258.e1. (PMID: 29428417) Genome Res. 2012 Sep;22(9):1813-31. (PMID: 22955991) Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801. (PMID: 29126249) Nat Biotechnol. 2008 Dec;26(12):1351-9. (PMID: 19029915) Genome Res. 2019 Nov;29(11):1900-1909. (PMID: 31645363) Bioinformatics. 2009 May 1;25(9):1105-11. (PMID: 19289445) Nat Rev Genet. 2009 Jan;10(1):57-63. (PMID: 19015660) Cell Genom. 2022 Jan 12;2(1):. (PMID: 35199087) Methods. 2009 Jul;48(3):240-8. (PMID: 19275939) Bioinformatics. 2013 Jan 1;29(1):15-21. (PMID: 23104886) Nat Methods. 2006 Mar;3(3):211-22. (PMID: 16489339) Sci Rep. 2019 Jun 27;9(1):9354. (PMID: 31249361) Nucleic Acids Res. 2020 Jan 8;48(D1):D882-D889. (PMID: 31713622) Bioinformatics. 2022 Mar 4;38(6):1729-1731. (PMID: 34978573) Bioinformatics. 2019 Jan 15;35(2):340-342. (PMID: 29912287) Mol Cell. 2016 Jan 7;61(1):170-80. (PMID: 26687680) Bioinformatics. 2018 Sep 15;34(18):3094-3100. (PMID: 29750242) Nature. 2020 Jul;583(7818):729-736. (PMID: 32728250) Cell. 2008 Jan 25;132(2):311-22. (PMID: 18243105) |
| معلومات مُعتمدة: | R01 HG009318 United States HG NHGRI NIH HHS; U24 HG009397 United States HG NHGRI NIH HHS |
| فهرسة مساهمة: | Keywords: NGS analysis; analysis pipelines; software |
| تواريخ الأحداث: | Date Created: 20230728 Latest Revision: 20240923 |
| رمز التحديث: | 20240923 |
| مُعرف محوري في PubMed: | PMC10371165 |
| DOI: | 10.21203/rs.3.rs-3111932/v1 |
| PMID: | 37503119 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 2693-5015 |
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| DOI: | 10.21203/rs.3.rs-3111932/v1 |