Here is waht I want to do:
I have an assembly (N50: 5774) from 454 data of a cyano bacteria genome of approximately 7Mb. As all my reads are sinlge end, I can not use mate pair information for scaffolding. However I have three genomes from related (same genus) sepcies. So I would like to use this information for scaffolding. My expirence with genome assemblies is very limited so I am not sure if this is even possible.
So my question is: Does it make sense to use genomes from realted (same genus) species to do scaffolding for a bacterial genome and if so, which tools could I use for that?