I have read from bovine papillomavirus and I mapped them to the Bovine papillomavirus type 1 (ncbi JX678969.1). I would like to visualize the reference genome, my mapped reads and annotation that is provided by ncbi.
In NCBI the genome is marked as linear, however I was told that it was circular.
I tried to visualize reads and the reference via Integrative Genome Browser, but it shows the a linear genome (I need a circular) and I cannot find how I can put my annotation list, so that I see which genes are there in my genome.
Is there any tool like IGV but for circular genome where I can per hand annotate the sequence?
5 answers
Take a look to the JAVA BRIG Ring Image Generator. It is very flexible and for sure can do what you are asking
As a standalone JAVA program, it runs in all OS
You can also try Genome Compiler: www.genomecompiler.com
It's free online and offline and works out perfect for these needs
Geneious will let you visualize circular annotated genomes. This functionality might be available in the free version (most basic manipulation and visualization is.)
Edit: I know you can visualized mapped reads against a reference designated as circular in Geneious Pro, but a license is not cheap. You might be able to do this in the free version.
You can have a look at Artemis, a slightly older genome Editor from Sanger. It reads GFF, GenBank, BAM... and performs okay for Viruses. It can produce circular maps with its DNAPlotter module quite easily.
Circos is perhaps the best visualization tool for circular genomes, but its leaning curve is quite steep. Another option could be AngularPlasmid.
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