Biostars

What’s the Answer? (visualize genomic rearrangements)

This week’s highlighted question at Biostars is a helpful summary of a number of tools available to solve this visualization problem. Although phrased in the form of a question, the original poster was actually providing a helpful list of the ones he’s investigated already, but he also wanted to know what was availble that others might be using. So it had content and generated some nice discussion on the subject as well.


Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Thursdays we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.


Question: Which program, tool, or strategy do you use to visualize genomic rearrangements?

In relation to my master thesis I’m working on tools to visualize fusion genes. In that regard I’m interested in any and all strategies and tools that exists for visualizing genomic rearrangements. I’ll include the list I have so far below, and update the list when I get answers.

Programming packages:

  • Circos: Perl package for circular plots, which are well suited for genomic rearrangements.
  • J-Circos is a java application for doing interactive work with circos plots.
  • ClicO FS: an interactive web-based service of Circos.
  • rCircos: R package for circular plots.
  • OmicCircos: R package for circular plots for omics data.
  • ggbio: R package for visualizing biological data. Has a circular view similar to the previous packages.
  • D3 chord diagrams (javascript) can be used to visualize genomic rearrangements. See this plot of migration flows as a similar example.

“Complete” tools:

[there's a series of images with examples here, I don't want to paste them all--go have a look]

stianlagstad

There were a number of additional tools listed in the comments. You should go over and look. And if you have other ones that are not yet over there, help a student out and add them.

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