Forum: Interesting/useful/beautiful bio sequence viz tools
6
gravatar for jrj.healey
10 months ago by
jrj.healey9.9k
United Kingdom
jrj.healey9.9k wrote:

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?!

EDIT:

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

visualisation forum python viz • 646 views
ADD COMMENTlink modified 10 months ago by SaltedPork80 • written 10 months ago by jrj.healey9.9k

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 10 months ago by jrj.healey9.9k
4
gravatar for dariober
10 months ago by
dariober9.8k
Glasgow - UK
dariober9.8k 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 10 months ago by dariober9.8k
4
gravatar for cmdcolin
10 months ago by
cmdcolin1.1k
United States
cmdcolin1.1k 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 10 months ago • written 10 months ago by cmdcolin1.1k
3
gravatar for Philipp Bayer
10 months ago by
Philipp Bayer5.9k
Australia/Perth/UWA
Philipp Bayer5.9k 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 10 months ago by Philipp Bayer5.9k
1
gravatar for SaltedPork
10 months ago by
SaltedPork80
SaltedPork80 wrote:

Circos and IGV I would recommend

ADD COMMENTlink written 10 months ago by SaltedPork80
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