How to produce an agp file

[Echo Chen]

Hi everyone,

I wonder if there is a pipeline for building an agp file from SOAPdenovo outputs for submission to Genbank (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml). 

At first I thought I could simply break the final scaffold file by N's, but then I realized that after the gap closing step, many scaffolds don't have any N's at all. I also looked at some other files that SOAPdenovo produced during the scaffolding step, but it is never straightforward to me how I could generate an agp file from them, especially when I used GapCloser after the scaffolding step.

Since so many successful SOAPdenovo assemblies have been published, I believe people have experience in producing the agp file. Thanks so much for your help. This has been bothering me for quite a while.

Echo