CoGe LoadExp+: A web‐based suite that integrates next‐generation sequencing data analysis workflows and visualization

• Published in: Plant direct Vol. 1; no. 2
• Main Authors: Grover, Jeffrey W., Bomhoff, Matthew, Davey, Sean, Gregory, Brian D., Mosher, Rebecca A., Lyons, Eric
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-07-2017; John Wiley and Sons Inc
• Subjects: Archives & records; Bioinformatics; Bisulfite; bisulfite sequencing; ChIP‐seq; Chromatin; Data analysis; DNA methylation; Epic literature; epigenomics; Experiments; expression analysis; Genomes; Genomics; Life sciences; Metadata; next‐generation sequencing; Original; Population genetics; Researchers; Ribonucleic acid; RNA; RNA‐seq; Single-nucleotide polymorphism; SNP identification; Visualization; population genetics; SNP identification; RNA‐seq; expression analysis; DNA methylation; epigenomics; genomics; bisulfite sequencing; next‐generation sequencing; ChIP‐seq
• ISSN: 2475-4455; 2475-4455
• DOI: 10.1002/pld3.8

Summary
To make genomic and epigenomic analyses more widely available to the biological research community, we have created LoadExp+, a suite of bioinformatics workflows integrated with the web‐based comparative genomics platform, CoGe. LoadExp+ allows users to perform transcriptomic (RNA‐seq), epigenomic (bisulfite‐seq), chromatin‐binding (ChIP‐seq), variant identification (SNPs), and population genetics analyses against any genome in CoGe, including genomes integrated by users themselves. Through LoadExp+'s integration with CoGe's existing features, all analyses are available for visualization and additional downstream processing, and are available for export to CyVerse's data management and analysis platforms. LoadExp+ provides easy‐to‐use functionality to manage genomics and epigenomics data throughout its entire lifecycle using a publicly available web‐based platform and facilitates greater accessibility of genomics analyses to researchers of all skill levels. LoadExp+ can be accessed at https://genomevolution.org.