How to visualize multiple bacterial genomes with circos?

Question

[marongiu.luigi]

I am trying to use circos to visualize the alignment of multiple bacterial genomes (essentially to create a genome atlas like this:

).

This software looks to me a bit of a language on its own right. What would be the syntax to run it?

I assume I will have a multiple alignment in fasta format and a gff3 file with the annotation. How do I run circos?

There is a lot of data on the configuration files (the heart of circos) but ho do I pass them to the main software? And how do I prepare the config files with the fasts/gff3 files?

Thank you

[biofalconch]

Not an answer but a suggestion, if you are more familiar with R maybe you want to give circlize a go :) https://jokergoo.github.io/circlize_book/book/

[marongiu.luigi]

I tried but there is no bacterial genome alignment...

[biofalconch]

You can do it without your Ideogram being established already in the database. I think it would go something like this: https://jokergoo.github.io/2020/10/16/concatenate-two-genomes-in-the-circular-plot/

[cmdcolin]

here is a pipeline that incorporates Circos that might help out https://github.com/robotoD/GenoVi see multiple genome tutorial https://github.com/robotoD/GenoVi/wiki/User-guide#tutorials-

Answer 1

[Binte.farooq]

For circos, follow the tutorials on the circos website (https://circos.ca/tutorials/course/). Tutorials are a little bit confusing but very helpfull. For syntax you need to follow tutorials.

To pass data to main software ( by main software you mean the circos config file ? ) you can simply create variables and pass on link to the data. For example you need karyotype for bacterial genome (to build rest of figure on it) and pass it on to a relevant variable like karyotype = user/circos/bac.karyotype.txt

and to plot your own data, you create tracks and pass input file location for that track using the variable 'file', for example

<plot>
type = histogram
r1 = 0.9r
r0 = 0.7r
file = user/circos/mutations_file.txt 
<\plot>

[mathavanbioinfo]

hi try this https://proksee.ca/