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Published July 1, 2023 | Submitted + Updated + Supplemental Material
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The ENCODE Uniform Analysis Pipelines


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 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/

Additional Information

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. We wish to thank all participants in the ENCODE Consortium for collaborations that have enhanced the metadata definitions, and the ENCODE Portal users for their useful feedback. Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under grant number U24-HG009397. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. All ENCODE primary and processed data are distributed for free via the Amazon Web Services (AWS; https://registry.opendata.aws/encode-project) and the ENCODE portal, https://www.encodeproject.org (a mirror of the data corpus also exists on the Microsoft Azure (https://learn.microsoft.com/en-us/azure/open-datasets/dataset-encode) cloud, courtesy of Microsoft and Terra. The authors have declared no competing interest.

Attached Files

Submitted - nihpp-2023.04.04.535623v1.pdf

Supplemental Material - media-1.pdf

Supplemental Material - media-2.pdf

Supplemental Material - media-3.pdf

Supplemental Material - media-4.pdf

Supplemental Material - media-6.pdf

Supplemental Material - media-7.pdf

Updated - media-5.pdf


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August 20, 2023
December 13, 2023