Forum: Interesting/useful/beautiful bio sequence viz tools
10
gravatar for Joe
2.7 years ago by
Joe18k
United Kingdom
Joe18k wrote:

Below is the previous post content, but I've just reformatted all this to a list now for easier future reference.

Looking for suggestions for tools generating nice viz outputs for various biological sequence data (e.g. plotting genome tracks with features).

So far I've come across:

They aren't quite as fully featured as I'd like (and BioGrapy is actually broken). Ideally I'd like programmatic tools (and python would be nice!), though GUIs are fine too. I have typically used ARTEMIS and SnapGene in the past, but they have little to no customisability.

Anyone come across things they really like?!

Some more I've come across from speaking to some other people!

visualisation forum python viz • 2.4k views
ADD COMMENTlink modified 9 months ago by statologycontact0 • written 2.7 years ago by Joe18k

I’ll add that, since these are going to be going in to a LaTeX doc, TeX packages are fair game too! I really like TeXShade for multiple sequence alignments for instance

ADD REPLYlink written 2.7 years ago by Joe18k
4
gravatar for dariober
2.7 years ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

Gviz is one more. I haven't played much with any of these tools but I haven't been impressed by any of them so far. I mean, they are great. But at the moment you want to customise your figures to make them publication quality they start falling short of what you need.

ADD COMMENTlink written 2.7 years ago by dariober11k
4
gravatar for Philipp Bayer
2.7 years ago by
Philipp Bayer6.8k
Australia/Perth/UWA
Philipp Bayer6.8k wrote:

I've had good experiences with karyoploteR https://github.com/bernatgel/karyoploteR It's an R-package that works similar to Circos (you got tracks with r0 and r1 and you put features onto those tracks)

Here's a gene density plot I made a while ago:

There's also a easier GUI version of Circos, but it costs money: http://omgenomics.com/circa/

ADD COMMENTlink written 2.7 years ago by Philipp Bayer6.8k
4
gravatar for cmdcolin
2.7 years ago by
cmdcolin1.4k
United States
cmdcolin1.4k wrote:

I think that the plugin and customization system of jbrowse allows you to make tons of things that are pretty cool, but having developed for them I'm sort of biased. Anyways, here are some examples of customized tracks in jbrowse made via plugins

multiple sequence alignment viewer https://github.com/cmdcolin/mafviewer

multiple bigwig plotter https://github.com/elsiklab/multibigwig

sashimi plots https://github.com/elsiklab/sashimiplot

gwas data https://github.com/elsiklab/gwasviewer

also https://github.com/bhofmei/ has many good plugins too

Other cool ones

IGV, IGV.js, BioDalliance, HiGlass, samplot, LocusZoom, the venerable gbrowse

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by cmdcolin1.4k

I started a large list here of lots of different types of viewers https://github.com/cmdcolin/awesome-genome-visualization/blob/master/README.md

ADD REPLYlink modified 9 months ago • written 9 months ago by cmdcolin1.4k

Ah, great, I was going to start an awesome-genome-viz-... type repository when I needed to procrastinate, but this is useful :)

Can I suggest you add contributing guidelines to keep everything consistent? I have a few in mind to add to that list.

ADD REPLYlink written 9 months ago by Joe18k

Sure, PRs are welcome. I added a little contributing.md file, basically anything is welcome though

ADD REPLYlink written 9 months ago by cmdcolin1.4k
1
gravatar for SaltedPork
2.7 years ago by
SaltedPork110
SaltedPork110 wrote:

Circos and IGV I would recommend

ADD COMMENTlink written 2.7 years ago by SaltedPork110
0
gravatar for statologycontact
9 months ago by
statologycontact0 wrote:

As others have mentioned, ggbio is a great tool. In addition, you can customize the themes in ggplot to take the viz as a whole to the next level. Here's a nice place to start if you're looking for some of the most aesthetically pleasing ggplot themes: https://www.statology.org/a-complete-guide-to-the-best-ggplot2-themes/

ADD COMMENTlink written 9 months ago by statologycontact0
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