PEGR: A management platform for ChIP-based next generation sequencing pipelines

Danying Shao, Gretta Kellogg, Shaun Mahony, William Lai, B. Franklin Pugh

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish (US)
Title of host publicationPEARC 2020 - Practice and Experience in Advanced Research Computing 2020
Subtitle of host publicationCatch the Wave
PublisherAssociation for Computing Machinery
Pages285-292
Number of pages8
ISBN (Electronic)9781450366892
DOIs
StatePublished - Jul 26 2020
Event2020 Conference on Practice and Experience in Advanced Research Computing: Catch the Wave, PEARC 2020 - Virtual, Online, United States
Duration: Jul 27 2020Jul 31 2020

Publication series

NameACM International Conference Proceeding Series

Conference

Conference2020 Conference on Practice and Experience in Advanced Research Computing: Catch the Wave, PEARC 2020
CountryUnited States
CityVirtual, Online
Period7/27/207/31/20

All Science Journal Classification (ASJC) codes

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

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