Software for visualizing circular genomes mapping

Question

[mmart12]

Hello,

Does anybody know a software for visualizing circular genome mapping against sequenced reads to see their distribution on the ref genome?

I already tried using circus but it does not work on Windows and I do not have the "make" function to have it working on mac.

Thank you

[Sukhi Singh]

Circos definitely works on windows and Mac plus "Make is a utility that automatically builds executable programs and libraries from source code by reading files called makefiles which specify how to derive the target program". So, it works with the makefiles inside the source code you download.

You need to install Xcode and developer tools for Make or if you just want the command line tools without Xcode, go here https://developer.apple.com/opensource/

[mmart12]

Hello, thank you for answer. Sorry, I mistyped, I meant Circus and it does not work on windows. I've been in contact with the developer.

About Mac, I cannot install Xcode as I have an older version of Mac OS (10.8) and the current Xcode works from OS 10.10 on.

[Sukhi Singh]

Ah Circos, just to answer the second part, you can definitely get older version of XCode, depending on your version else you can use RCircos for quick plotting, you don't need the local installation of complete tool then. Also checkout, I think its already answered here.

Answer 1

[h.mon]

Try BLAST Ring Image Generator, or BRIG for short. Should work on Windows.

[mmart12]

I already tried BRIG but it does not generate the alignment. I guess it is because I have thousands of short reads to map to the reference (which represent insertions in transposons) and not a draft/complete genome

[h.mon]

Can't you use IGV for that?

[mmart12]

I actually solved by using CGview.