User-Friendly Whole Genome DNA Methylation Analysis With FlowGe

Acquiring the specialized knowledge and resources required to manage, process, analyze, and visualize data from next generation sequencing (NGS) experiments is a bottleneck for many researchers. To address this issue we have integrated a suite of bioinformatics workflows into the web-based comparative genomics platform, CoGe. We term CoGe’s integrated NGS workflows FlowGe. FlowGe’s workflows include RNAseq, whole-genome bisulfite sequencing, ChIP-seq, variant calling (SNPs), and population genetics calculations. Unlike other standalone next-generation sequencing applications, FlowGe leverages the over 27,000 genomes currently available within CoGe and enables users to take advantage of CoGe’s intuitive user interface. This facilitates rapid data processing, and integration of visualization and analysis in a single platform. Importantly, FlowGe allows researchers to control access to their data and share it with others, as well as combine public and private NGS data to answer genome-scale questions. CoGe’s genome visualization system, NGS analysis workflows, and its connection to the CyVerse Data Store provide an integrated ecosystem to manage NGS data throughout its life cycle and facilitate greater accessibility of genomics analyses to researchers of all levels. To demonstrate FlowGe’s ease of use and utility to all researchers we will demonstrate analysis of whole-genome bisulfite sequencing data to determine global DNA methylation levels.

FlowGe is freely available on the web at https://genomevolution.org under the MIT open source license (source code on GitHub https://github.com/LyonsLab/coge).