Set Up Soapdenovo (Or Just A Fasta File Of Scaffolds) For Ncbi Wgs Genome Submission

Question

[John St. John]

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?

Thanks!

[tsucheta]

Hi,

I want to generate files for genbank submission especially agp files. While I can write a simple perl script for that, but I would still prefer a tool that does this job. You mentioned about some tool in allpaths exactly does this, but I dont find it from the manual. If you could tell me which one does this will be great.

Answer 1

[Nick Loman]

I believe that NCBI will waive the minimum contig size requirement if it forms part of a scaffold. If the contig is an unlinked singleton then I think they prefer contigs >200bp. This is the relevant guide although it is not explicit about that (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/submission/faq.shtml).

Answer 2

[hersteinj]

I had a question about how you converted your SOAPdenovo assembly to an AGP file. I'm trying to submit a genome to NCBI WGS genome stie but I'm not sure how to generate an AGP file from the scaffolds. Could I ask how you accomplished that?

Thanks!

[John St. John]

I used this: https://github.com/jstjohn/KentLib/tree/master/examples/hgFakeAgpForNcbi however I believe the requirements changed so that would need to be modified and I do not have the time to do it.