Actually my assembly started off with Allpaths-lg rather than SOAPdenovo, but then I modified the assembly using a few external tools. Allpaths has a great tool for preparing its own assemblies for NCBI submission, but once I modified the assembly I don't have that ability anymore. Right now I am at the same place someone would be once they did a SOAPdenovo assembly. I have a scaffold file, and that is it. I can convert to contigs+agp just fine, but some of my contigs are less than the minimum length requirement. Removing those would require modifying the associated AGP file, and things just start getting complicated at that point. I can do it, but I am hoping that there are standard tools out there already.
I am guessing there are tools out there to prepare soapdenovo assemblies to be submitted to the NCBI WGS genome site (since there are multiple SOAPdenovo assemblies up there already). I am having trouble finding them on google, or seqanswers. Could someone point me in the right direction?