Contig order on Genbank

[PhDiddy]

A bacterial species I am interested in has had it genome sequenced but is only available as contigs on Genbank. These contigs are numbered. Can anybody tell me if these contigs are in order?

I want to upload them to RAST and am wondering can they just be uploaded as is from genbank.

Thanks

[GenoMax]

Unless something has changed the contigs are not likely to be "ordered" meaningfully (other than perhaps largest to smallest or vice-varsa) for an "unfinished" genome. You may need to dig through the supplementary material associated with the submission to see if there is any information.

[PhDiddy]

Thanks genomax.

If I use a tool such as emboss union will this order the contigs for me? I tried mauve but I keep getting an error. I can input the contigs to emboss union which gives me 1 full sequence for all removing the overlapping regions.

I am pretty new to all this and my basis is that if it joins them in a way that removes the overlapping regions then they are in the correct order. But I could be way off base!

[GenoMax]

If the contigs are truly overlapping this easily then the folks who originally submitted the sequence would have discovered that (unless this was an automated whole genome survey type sequence submission). But since they did not perhaps there was a reason.

Is there a closely related genome available (that is "finished"/annotated) in GenBank? If there is then you could compare the contig resulting from Emboss union to the finished genome. Just because an informatics tool produced an output does not mean that the result is right. This is where domain knowledge expertise needs to come in to decide if the result looks reasonable/acceptable.