Forum: Interesting/useful/beautiful bio sequence viz tools
5
gravatar for jrj.healey
6 months ago by
jrj.healey6.8k
United Kingdom
jrj.healey6.8k 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 • 466 views
ADD COMMENTlink modified 6 months ago by SaltedPork80 • written 6 months ago by jrj.healey6.8k

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 6 months ago by jrj.healey6.8k
3
gravatar for Philipp Bayer
6 months ago by
Philipp Bayer5.6k
Australia/Perth/UWA
Philipp Bayer5.6k 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 6 months ago by Philipp Bayer5.6k
2
gravatar for dariober
6 months ago by
dariober9.4k
Glasgow - UK
dariober9.4k 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 6 months ago by dariober9.4k
2
gravatar for cmdcolin
6 months ago by
cmdcolin870
United States
cmdcolin870 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 6 months ago • written 6 months ago by cmdcolin870
1
gravatar for SaltedPork
6 months ago by
SaltedPork80
SaltedPork80 wrote:

Circos and IGV I would recommend

ADD COMMENTlink written 6 months ago by SaltedPork80
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