Re: [Gmod-ajax] Synteny Viewer

[Colin <col...@gm...>]

Hi Hans, I'm not aware of anything for jbrowse 1 but we would certainly be
happy to help with jbrowse 2. Currently the synteny view in jbrowse 2 can
compare just two genomes at a time, but definitely interested in extending
this

It could be helpful to know that jbrowse 2 can load the anchors file from
the mcscan pipeline
https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version) also which
I think your figure refers to

-Colin

On Thu, May 19, 2022, 12:07 AM Hans Vasquez-Gross <hva...@un...>
wrote:

> 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
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
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