replicate SyRi/plotsr output plot in R

Question

[Matteo Ungaro]

Hi I'm working on some genomes for which I'm computing synteny against a reference. For the main analyses I'm using SyRi which is a very nice tool and provide plotting options through the plotsr package.

However, for this work we intend to display structural rearrangements between both haplotypes for these genomes against the reference in a single plot with one on top and the other at the bottom (with the reference genome in the middle).

Is there a way to do so starting from the SyRi .out file which is the one the tools uses for plotting? Also, if this could be ported to R since plotsr is written in Python which I'm less comfortable with. If anyone has any experience with this analyses any help is much appreciated, thanks!

Answer 1

[cmdcolin]

a couple pure R options include SVbyEye, ntSynt, and chromSyn

here is a short list of tools I've tagged as 'multi-way synteny' and 'R' https://cmdcolin.github.io/awesome-genome-visualization/?language=R&latest=true&tag=Multi-way%20synteny

these likely do not use the .out file format, SVbyEye for example ingests minimap2 paf, but you could try to roll your own methods also

[samuel.a.odonnell]

Alternatively, if you are comfortable with R, you could use all the functions within gggenomes to generate ribbon-like plots of multiple haplotypes vs a reference and highlighting SVs called by Syri

[cmdcolin]

thanks for this note. I added gggenomes to the 'multi-way synteny' tag. note also that ntsynt uses gggenomes under the hood so is a nice helper package