Simple alternatives for the program Circos

Question

[gabri]

Dear All,

I have an assembly with a certain number of scaffolds separated at chromosome level. I'd like to draw a very simple circular picture in which I can represent each chromosome with the associated scaffolds. I know that one of the most used software for these kinds of circular pictures is Circos. However, it looks very complex and I need a very simple picture compared to these produced by Circos. Are there any good simpler alternatives?

Thanks

[archana.bioinfo87]

Hi,

You can also try symap. See this link

http://www.agcol.arizona.edu/software/symap/

May be it will help you.

[Joe]

You just want to show them arranged circularly or you want to actually do some analysis/comparison etc?

[gabri]

Yes I just want to show them arranged circularly. Thanks

[gabri]

https://ibb.co/gDeYcz

Thanks for all the suggestions. Here I put a very simple example that I manually drew to let you know what I mean. The external cirle with different colours represents the chromosomes (sequences that I don't have), the black circle inside represents the scaffolds (the sequences that I have). My multifasta file has headers like these:

Seq1_Chromosome1

Seq2_Chromosome1

Seq3_Chromosome1

Seq4_Chromosome2

Seq5_Chromosome2

Seq6_Chromosome2

Seq7_Chromosome3

Seq8_Chromosome3

Seq9_Chromosome3

Seq10_Chromosome4

Seq11_Chromosome4

So I need a program that separate my sequences into a circular rapresentation using the information in the headers.

Thanks again.

[jared.andrews07]

For future reference, if you're trying to reply to an answer, use the 'Add Comment' button below the answer rather than posting your comment as an answer. It will help to keep things organized. A moderator will likely move this to a comment to my answer above if they take a look at this question.

If that's what you're trying to do, I think any of the options above will work - they all have examples similar to that in their galleries. You will likely have to BLAST your sequences against the actual reference genome to get the positions of your sequences first though. Throwing sequence data at a Circos plot doesn't work well, but genomic ranges will work just fine.

[Joe]

A moderator will likely move this to a comment to my answer above if they take a look at this question.

And so it was.

[Joe]

I'm pretty certain you aren't going to find a tool that generates exactly what you're looking for easily. For once, circos probably is the best option, but you're going to have to use walkthroughs online to get comfortable with writing the config file needed.

You might be able to get in touch with the Circos developer(s) for help.

Answer 1

[Pierre Lindenbaum]

i wrote something: http://lindenb.github.io/jvarkit/Biostar336589.html

example: plotting the 'gap' regions in the UCSC

plotting some genes

Answer 2

[jared.andrews07]

Can you post an example of what you're looking to do? Will make it easier to give suggestions. These are several R packages capable of this though - OmicCircos, circlize, and shinyCircos, which runs in a web browser.