PEGR: a management platform for ChIP-based next generation sequencing pipelines
Authors: 
Danying Shao, 
Gretta Kellogg, Shaun Mahony, William Lai, B. Franklin PughAuthors Info & Claims
Danying Shao, Gretta Kellogg, Shaun Mahony, William Lai, B. Franklin PughAuthors Info & ClaimsPages 285 - 292
Abstract
There has been a rapid development in genome sequencing, including high-throughput next generation sequencing (NGS) technologies, automation in biological experiments, new bioinformatics tools and utilization of high-performance computing and cloud computing. ChIP-based NGS technologies, e.g. ChIP-seq and ChIP-exo, are widely used to detect the binding sites of DNA-interacting proteins in the genome and help us to have a deeper mechanistic understanding of genomic regulation. As sequencing data is generated at an unprecedented pace from the ChIP-based NGS pipelines, there is an urgent need for a metadata management system. To meet this need, we developed the Platform for Eukaryotic Genomic Regulation (PEGR), a web service platform that logs metadata for samples and sequencing experiments, manages the data processing workflows, and provides reporting and visualization. PEGR links together people, samples, protocols, DNA sequencers and bioinformatics computation. With the help of PEGR, scientists can have a more integrated understanding of the sequencing data and better understand the scientific mechanisms of genomic regulation. In this paper, we present the architecture and the major functionalities of PEGR. We also share our experience in developing this application and discuss the future directions.
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July 2020
556 pages
ISBN:9781450366892
DOI:10.1145/3311790
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Published: 26 July 2020
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PEARC '20: Practice and Experience in Advanced Research Computing
July 26 - 30, 2020
OR, Portland, USA
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