Justin Chu

Has been added to conda: https://github.com/bioconda/bioconda-recipes/pull/49318

The pipeline essentially uses a base circos configuration file. Changing values like: https://github.com/JustinChu/JupiterPlot/blob/215dd386797252fe928e60745529939649787c4b/jupiterplot/config/rawConf.conf#L13 https://github.com/JustinChu/JupiterPlot/blob/215dd386797252fe928e60745529939649787c4b/jupiterplot/config/rawConf.conf#L23 should help you get what you need but it will take some tweaking of this file...

Also, rather than altering the master file altering the prefix.conf file produced and re-running the rendering step is probably the way to go.

At the most basic level, grey links denote the start and end of link bundles. Even the large regions have grey lines at the start and end points of contiguous...

Interesting. So you have been doing reference guided scaffolding. If that is the case it makes sense why the results are so much cleaner on the second plot. Indeed the...

I did some testing on long reads in 2020, with some results on a BCGSC Jira ticket. I think the results were pretty good and with modern Nanopore accuracy improved...

Is it similar to this issue? https://github.com/JustinChu/JupiterPlot/issues/47#issuecomment-2313545217 Basically tweaking the radius of the circle can help since the labels are rendered based on that. It's a common enough issue I...