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Interesting/useful/beautiful bio sequence viz tools
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3 months ago
Joe 12k
United Kingdom

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!

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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

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13 months ago
WCIP | Glasgow | UK

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.

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14 months ago
cmdcolin ♦ 1.2k
United States

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

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11 months ago
Australia/Perth/UWA

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/

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12 months ago
SaltedPork • 100

Circos and IGV I would recommend

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