I started a large list here of lots of different types of viewers https://github.com/cmdcolin/awesome-genome-visualization/blob/master/README.md
Forum: Interesting/useful/beautiful bio sequence viz tools
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!
GenoPlotr (An R solution)
GenomeDiagrams (part of BioPython already which is nice)
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Yannick Wurm
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Joe
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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.
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:
Gene densities of published B. rapa, oleracea, napus genomes plotted using @bernatgel 's karyoploteR and RColorBrewer, so pretty
— Philipp Bayer (@PhilippBayer) February 4, 2018
If someone can think of a way to 'normalise' all pseudomolecule lengths I'd be happy :P Right now I get 'holes' from shorter pseudomolecules.... pic.twitter.com/tDwEUS8OFn
There's also a easier GUI version of Circos, but it costs money: http://omgenomics.com/circa/
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Philipp Bayer
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
For those who like point-and-click tools, allow me to mention that our SequenceServer software has a bunch of useful visualization mechanism built in for BLAST alignments. It include kablammo-style pairwise alignments, circus plot, and a bunch of others.
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Yannick Wurm
Circos and IGV I would recommend
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SaltedPork
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/
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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