Forum:Interesting/useful/beautiful bio sequence viz tools

Question

[Joe]

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:

• BioGraPy

• pyGenomeTracks

• ggbio

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!

• BioGraPy

• pyGenomeTracks

• ggbio

• GenoPlotr (An R solution)

• GenomeDiagrams (part of BioPython already which is nice)

• Kablammo

• DNAFeaturesViewer

• BRIG

• EasyFig

• Sibelia

• DNAplotlib

• Clinker

[Joe]

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

Answer 1

[dariober]

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.

Answer 2

[Philipp Bayer]

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
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

— Philipp Bayer (@PhilippBayer) February 4, 2018

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

Answer 3

[cmdcolin]

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

[cmdcolin]

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

[Joe]

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.

[cmdcolin]

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

Answer 4

[Yannick Wurm]

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.

Answer 5

[SaltedPork]

Circos and IGV I would recommend

Answer 6

[statologycontact]

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/