Draw a genome map with CGView server?

Question

[El Niño]

Hi everyone,

I am a bioinformatics newbie. I was asked to draw a genome map of a strain of bacteria whose complete genome sequence has been worked out. However, when I put my .fasta file onto the website CGView server, it showed only the longest contig (~280KB) on the circular genome map, while in fact my whole genome is around 5.8MB long.

What happened? Does anybody know how to solve this problem? Thank you a bunch. The genome assembly part was done by another lab using SOAP denovo. The assembly results give 201 contigs.

[Pierre Lindenbaum]

use another tool like circos ?

[El Niño]

Yeah, should be that. But I still need to know why my data cannot generate a full genome map? Do you have any idea?

[bioprodatviet]

I am also drawing bacterial cicular genome map based on WGS of more than 1000 contigs. Which tools should I use for drawing bacterial cicular map capable able of being used for paper publication. Thanks for your kind supports!

[Max Sikolenko]

Circular genome maps of unassembled contigs do not make much sense, unfortunately. Anyway,

Which tools should I use for drawing bacterial cicular map capable able of being used for paper publication.

The only honest and decent way is to finish the assembly: assemble the contigs into complete genome sequence(s). If there are no plasmids in the genome, then it should be a single (typically circular) chromosome sequence.