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

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.

A high-resolution protein architecture of the budding yeast genome

“…Additional previously published ChIP-exo datasets for Hsf1, Msn2, Spt15, Spt16, Ifh1, and Fhl1 were included in data processing and analysis for this study 23 , 36 . Data were managed, quality controlled, and processed through a custom automated workflow control called PEGR (Platform for Epi-Genomic Research) 38 . Sequence reads were aligned to the yeast (sacCer3) genome using bwa-mem (v0.7.17) Aligned reads were filtered using Picard (v2.7.1) 39 and samtools (v0.1.18) 40 to remove PCR duplicates (i.e., where the 5’ coordinates-strand of Read_1 and Read_2 were identical to another read pair), and non-uniquely mapping reads.…”

PEGR: a flexible management platform for reproducible epigenomic and genomic research

“…Previously, we presented a proof-of-concept vision of PEGR software [23]. We now present a fully functional and open-source version of PEGR software, including streamlined experiment tracking with reagent barcoding, flexibility for multiple heterogeneous bioinformatics workflows, and a project management approach.…”

“…It supports Findable, Accessible, Interoperable and Reusable (FAIR) best practices by tracking the metadata throughout the entire sequencing pipeline to enable experimental reproducibility [22]. Previously, we presented a proof-of-concept vision of PEGR software [23]. We now present a fully functional and open-source version of PEGR software, including streamlined experiment tracking with reagent barcoding, flexibility for multiple heterogeneous bioinformatics workflows, and a project management approach.…”

PEGR: a flexible management platform for reproducible epigenomic and genomic research

“…It supports Findable, Accessible, Interoperable and Reusable (FAIR) best practices by tracking the metadata throughout the entire sequencing pipeline to enable experimental reproducibility [ 29 ]. Previously, we presented a proof-of-concept vision of PEGR software [ 30 ]. We now present a fully functional and open-source version of PEGR software, including streamlined experiment tracking with reagent barcoding, flexibility for multiple heterogeneous bioinformatics workflows, and a project management approach.…”