Question: Reordering contigs of circular genome
0
gravatar for agata88
19 months ago by
agata88790
Poland
agata88790 wrote:

Hi all!

Finally I went trough contamination in bacteria genome (circular) , and now I would like to reorder contigs (less than 20). I used mauve contig mover for this purpose (http://darlinglab.org/mauve/user-guide/reordering.html). I am not sure if it is a good solution cause my bacteria is novel and it's hard to define the closest species. Anyway I have ordered contigs where 7 of them are "Contigs with conflicting ordering information". This means that I cannot say whether those 7 contigs are welled ordered.

I was trying to map contigs into possible closest one species and then see what is the ordering, but it ended up with a lot of multiple aligments and breaks.

I would like to annotate contigs with prokka, but to do that I need to know the ordering of contigs to not miss any genome element.

How can I order contigs to make results reliable annotated?

Many thanks, Agata

mauve • 749 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by agata88790

If there isnt a closely related closed genome, contig reordering is largely arbitrary anyway. Its mostly done for convenience when people go hunting for particular genes etc. Mauve is a perfectly valid tool to do it.

Ordering your contigs makes no difference to prokka, other than paralogs will be numbered in the order they appear in the contigs file top to bottom.

ADD REPLYlink modified 19 months ago • written 19 months ago by Joe16k
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