The ENCODE Uniform Analysis Pipelines
Author:
Hitz Benjamin C.ORCID, Lee Jin-WookORCID, Jolanki OttoORCID, Kagda Meenakshi S.ORCID, Graham KeenanORCID, Sud PaulORCID, Gabdank IdanORCID, Seth Strattan J.ORCID, Sloan Cricket A.ORCID, Dreszer TimothyORCID, Rowe Laurence D.ORCID, Podduturi Nikhil R.ORCID, Malladi Venkat S.ORCID, Chan Esther T.ORCID, Davidson Jean M.ORCID, Ho MarcusORCID, Miyasato StuartORCID, Simison MattORCID, Tanaka ForrestORCID, Luo YunhaiORCID, Whaling IanORCID, Hong Eurie L.ORCID, Lee Brian T.ORCID, Sandstrom RichardORCID, Rynes EricORCID, Nelson JemmaORCID, Nishida AndrewORCID, Ingersoll AlyssaORCID, Buckley MichaelORCID, Frerker MarkORCID, Kim Daniel SORCID, Boley NathanORCID, Trout DianeORCID, Dobin AlexORCID, Rahmanian SorenaORCID, Wyman DanaORCID, Balderrama-Gutierrez GabrielaORCID, Reese FairlieORCID, Durand Neva C.ORCID, Dudchenko OlgaORCID, Weisz DavidORCID, Rao Suhas S. P.ORCID, Blackburn AlyssaORCID, Gkountaroulis DimosORCID, Sadr MahdiORCID, Olshansky MosheORCID, Eliaz YossiORCID, Nguyen DatORCID, Bochkov IvanORCID, Shamim Muhammad SaadORCID, Mahajan RaginiORCID, Aiden ErezORCID, Gingeras TomORCID, Heath SimonORCID, Hirst MartinORCID, James Kent W.ORCID, Kundaje AnshulORCID, Mortazavi AliORCID, Wold BarbaraORCID, Cherry J. MichaelORCID
Abstract
AbstractThe 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 theHomo sapiensandMus musculusgenomes. 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 availableviathe 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 environmentsviaCromwell. Access to the pipelines and dataviathe 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.Database URL:https://www.encodeproject.org/
Publisher
Cold Spring Harbor Laboratory
Cited by
11 articles.
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