Question: Set Up Soapdenovo (Or Just A Fasta File Of Scaffolds) For Ncbi Wgs Genome Submission
gravatar for John St. John
7.4 years ago by
John St. John1.1k
San Francisco, CA, Cancer Therapeutics Innovation Group
John St. John1.1k wrote:

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?


genome ncbi • 2.5k views
ADD COMMENTlink written 7.4 years ago by John St. John1.1k


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.

ADD REPLYlink written 5.0 years ago by tsucheta0
gravatar for Nick Loman
7.4 years ago by
Nick Loman610
United Kingdom
Nick Loman610 wrote:

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 (

ADD COMMENTlink written 7.4 years ago by Nick Loman610
gravatar for hersteinj
7.0 years ago by
hersteinj0 wrote:

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?


ADD COMMENTlink written 7.0 years ago by hersteinj0

I used this: however I believe the requirements changed so that would need to be modified and I do not have the time to do it.

ADD REPLYlink written 6.8 years ago by John St. John1.1k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2419 users visited in the last hour