Sorry for that undetailed post, but I suggest you to look at Circos software:

http://circos.ca/

I work on plastid DNA which can be represented in circular form; this tools it's very powerful for that ! I suggest you to treat your contigs as chromosomes. The online doc and tutorial will be very helpful, more than this post.

Regards,

Rémi

Circos is difficult to understand. But it would great if you please tell me that is it necessary to have single genome sequence file in order to draw the circular map? In my case I have 50 fasta files (contigs)

Thanks

I could see that a related genome of Anoxybacillus flavithermus WK1 is available on NCBI. IN that case you can use BRIG tool (http://brig.sourceforge.net/) to show your assembly contigs against WK1 genome as reference. As an alternative you can use CGview to plot your contigs. 

Unless you know the order of the contigs, showing them as a circle is somewhat of an arbitrary decision. If you do choose to do so I would recommend making some indication of where contig/scaffold boundaries are.

Are you sure you can't upload a multisequence fasta file into DNAplotter? Have you tried? I know that ACT and ARTEMIS have no problem reading these. Students in my class do this regularly. To show the gene annotations, you'll need a corresponding *gff file which can easily be generated in Excel from whatever annotation files you have (see reference on gff format here https://www.sanger.ac.uk/resources/software/gff/spec.html)

If using a multisequence fasta file does not work, you can fake out DNAplotter, by 1) concatenating your individual contigs into a single pseudochromosome then 2) make a *gff file with coordinates to match. Basically your gene coordinates for contig1 would all be the same, then for contig2 you would add the length of contig1 to each of the coordinates, contig3 you add the combined length of contig1 & contig2 and so on. Again making this gff file can be readily done in Excel.

Dear Patrick

Thank you for your detailed reply. I hope I will find some way to manage it now.

Besides, what do you mean by multisequence fasta file? Is it single file prepared after merging sequences of different contigs (megacontig)? Or you are saying to upload all the fasta files for each contig separately in the software. 

Dear Muhammad Arslan,

If your genome has been deposited in the Genbank, you can try out our template based circular plot generator called CLICOFS. Just import you genbank formatted file to generate your circular plot. Its free to use as well.

http://codoncloud.com:3000/

As I know Geneious is able to do it but it is commercial

Hi Muhammad Arslan,

You may try Circos or ClicO FS.

Circos is very powerful tool but it required an installation and running in command-line interface, whereas ClicO-FS is a web service, was developed based on Circos, with user interface.

For your case, it only required to prepare 3 files to use ClicO-FS:

1. Karyotype File. 7 columns txt files containing the 50 contigs information like name and size.

2. Forward Genes. 3 columns txt: (1) Contigs ID, (2) Coordinate Start, (3) Coordinate End.

3. Reverse Genes. 3 columns txt: (1) Contigs ID, (2) Coordinate Start, and (3) Coordinate End.

You just have to visit website ClicO-FS: clicofs.codoncloud.com

and follow on-screen instruction

Feel free to text me if you need help on this.

#########

I tried to plot it based on the information that you provided.

Here are the files used and output figure.

You can modify the figures and colour as you like, based on following link:

http://codoncloud.com:3000/projects/35/karyotypes

clicofs.codoncloud.com

Hi Yung-Chie Tan and Choong Chee Hoh,

I recently tried to use your application ClicO FS online and I cannot access the official website anymore. Would you have different links or ways to access the tool?

Thanks in advance,

Ana

Hi Ana,

Thanks for your question. I have followed up with our team and I'm confident that your problem is resolved now? Please do not hesitate to contact us should you run into problems using our applications again. Thanks for using clico!

ivan

Hi again, Ivan.

I was recently trying to use ClicO FS again to generate genomic plots and I could not access it online. Would you have an updated link to access the tool? Thanks!

Hi Ana, it is working.

http://codoncloud.com:3000/get-started

Thanks a lot, Muhammad!

Choong Chee Hoh , Hi, I can not access clico FS at all. The website never worked for me at all.

I am trying to draw circos to show structural variations of an isolate. I am having difficulty getting the karyotype file. Any easy way to draw karyotype file?

Thanks

How can I draw a circular genome map for the complete genome sequence of moths species?

Choong Chee Hoh , I could use it using a VPN from India. Institutional networks have some problems.

Hi rémi Maglione . Thanks the tip. I have assembled genome with 11 contigs. From the suggestions above using circos will mean to generate karyotype file. Since you have some experience with using it , I will be grateful if you could briefly demonstrate how to generate the karyotype.

PS:

I annotated the draft assembly using prokka and therefore I have the .gbk file as well

Hi

I want to show the interaction between miRNA and their target and the pathway they involved. How can I prepare a file to upload?

Thank you for your help

ClicO-FS is not working. After uploading the GenBank file of a bacterial WGS, it is showing an error has occurred.

I wonder if anybody knows how to create a karyotype file for a 7 contig bacterial genome or if someone could give me an example of the files required to get a bacterial genome circular plot using ClicO FS. Thanks in advance