Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Wednesday Speaker Abstracts

Portable and Reproducible Computational Analyses Idan Gabdank 1 ; Esther Chan 1 ; Jason Hilton 1 ; Weiwei Zhong 1 ; Seth J Strattan 1 ; Yunhai Luo 1 ; Ulugbek K Baymuradov 1 ; Timothy R Dreszer 1 ; Otto A Jolanki 1 ; Keenan Graham 1 ; Kathrina C Onate 1 ; Nicholas Luther 1 ; Zachary A Myers 1 ; Stuart R Miyasato 1 ; Forrest Tanaka 1 ; Philip Adenekan 1 ; Karthik Kalyanaraman 1 ; Benjamin C Hitz 1 ; Michael J Cherry 1 ; 1 Stanford, Genetics, Palo Alto, California, United States The Encyclopedia of DNA Elements (ENCODE) project is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The main goal of the project is to identify all of the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) collects, curates, and disseminates the results, methods, and raw data for a variety of complex assays and analyses that have been performed to identify and validate these elements. In order to achieve transparent, reproducible, and comparable analysis results the ENCODE DCC has established a framework for the development and implementation of computational processing pipelines. Docker, for software containerization, and WDL, for workflow description, are used to develop modular and scalable pipelines that run identically on multiple compute platforms. Continuous integration methodologies are used to automate pipeline testing and deployment. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses. ENCODE uniform processing pipelines are available or in development for the analysis of ChIP- seq, RNA-seq, DNase-seq, ATAC-seq, HiC, ChIA-PET, and WGBS assays. The pipelines are open-source and have unified documentation. The ENCODE DCC codebase is at https://github.com/ENCODE-DCC

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