[Gmod-ajax] Synteny Viewer

[Hans Vasquez-G. <hva...@un...>]

Hello All,

I have a couple questions regarding Synteny visualization. I saw that JBrowse2 has a dot plot and linear view for synteny. Are there similar plugins for JBrowse1? Currently, I am running JBrowse1, but I am willing to also install JBrowse2 for this project.

In the linear view, is there a way to have multiple genomes visualized? I have a denovo assembly of haplotype phased data (2 FASTA files) as well as a closely related denovo assembly, that I would like to visualize with the Sorghum reference.

I found another program that can generate a figure with multiple genomes (example<https://camo.githubusercontent.com/833e373b369f1c221132d729e1cf0128a8cd638fc04c90782ad7d5e9d30867db/68747470733a2f2f7777772e64726f70626f782e636f6d2f732f39766c337973336e6476696d6734632f67726170652d70656163682d636163616f2e706e673f7261773d31>), but was wondering if JBrowse2 can do this.

Thank you,
-Hans


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[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>