EPIC-CoGe: Functional and Diversity Comparative Genomics

Have genomes; need help with downstream analyses?

This workshop provides an overview and in-depth examples of the comparative genomics platform CoGe (http://genomevolution.org) focusing on:

• Managing your genome:  How to add your own genome to CoGe, add structural and functional annotations, keep it private, share it with collaborators, and make it fully public (http://genomevolution.org/r/8kzz)
• Integrating functional and diversity data:  The EPIC-CoGe addition enables researchers to integrate RNASeq, BS-Seq, ChIP-Seq, DNA resequencing data, microarrays, and any other type of quantitative genomic measurements to any genome in CoGe (http://genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial)
• Having your own genome browser instantly:  The EPIC-CoGe genome browser, based on JBrowse, is instantly available for any genome and associated data loaded into CoGe (http://genomevolution.org/r/9xjy) 

These features are in addition to CoGe's stand features of:

• Whole genome comparisons: Identify and classify orthologous and paralogous genes, identify whole genome duplications, use synteny to order and orient contigs and scaffolds against any reference genome to create pseudo-assemblies
• Micro-synteny analyses: Identify gene model errors, conserved non-coding sequences, tandem gene duplications, and changes in local genome structure
• Multiple whole genome synteny analyses: Given a gene in one genome, find syntenic regions across multiple genomes, even if that specific gene is not present.

CoGe offers a multitude of advanced on-the-fly analyses.  To accomplish these, CoGe is part of the Powered by iPlant Program and leverages iPlant’s Cyberinfrastructure for computational scalability.  Learn more about this program at: http://www.iplantcollaborative.org/discover/powered-by-iplant

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