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GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
204 stars 61 forks source link

Add gGraph-style visualizations #2434

Open rbuels opened 2 years ago

rbuels commented 2 years ago

The breakpoint split view is a good first step, but we need more powerful tools to understand more complex rearrangement events.

Figure idea: https://www.nature.com/articles/s41586-019-1913-9/figures/3 Tool that makes similar figures: http://mskilab.com/gGraph/

A paper with more crazy rearrangement stuff: https://www.biorxiv.org/content/10.1101/2020.10.15.340497v1.full.pdf

cmdcolin commented 2 years ago

to me, the "possible derived chromosome" is one of the best part of the figures....being able to correctly get the derived chromosome and even get things like a gene track mapped over to that would be amazing, and is something I think will become bigger along with "assembly based SV calling"

rbuels commented 2 years ago

i.e. use synteny style views to look at the rearranged genome vs the reference, and see genes and other annotations mapped to it, or at least on the other side of the synteny relationship

rbuels commented 2 years ago

Needs more brainstorming.

cmdcolin commented 9 months ago

I think that this issue doesn't have any concrete proposals. I will just title this: gGraph style visualizations instead (coverage + arcs connecting breakpoints in a single track essentially)