PanGenome Visualization with JBrowse

PanGenome Visualization with JBrowse

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Namita Dongre, Anika Verma, Indresh Singh

 


The objective of this project was to visually compare genome variations to a single consensus using a genome browser.  Our biological data came from the Enterobacter cloacae, strain 34977 and was based on the pan-genomic analysis done by pan-genome ortholog clustering tool (PanOCT) and three other commonly used ortholog-detection methods. Our consensus track contained the 70% common clusters present in the various genomes of E. cloacae. We created GFF-file format tracks for the consensus and individual genomes with Python and imported them into JBrowse, a JavaScript-based genome browser. We also prepared a reference sequence FASTA file which contained sequence data for the consensus track. Our JBrowse customizations allow users to easily view and compare clusters, flexible genome island (fGI) inserts, and other special features present in the consensus and genome variants.