Answers.Body: <p>You should use a liftover approach. You could either do this based on exact changes, which might be a bit tedious given the presumably large number of join operations you've done (especially if you've e.g. broken contigs).</p>
  <p>Therefore it might be more convenient to do it on the basis of homology.</p>
  <p><a href="https://github.com/agshumate/Liftoff" rel="nofollow noreferrer">liftoff</a> is one simple tool for doing this with a gff file and your 2 fasta files. It seems to mostly work ok.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-02T23:23:34.543Z
Answers.LastActivityDate: 2021-09-02T23:23:34.543Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length assemblies. How do I annotate the output .fasta from the optical mapping assembly using the .gff of the draft assembly that was used as input? I also have a .agp file that describes what sequence fragments ended up where in the output.</p>
  
Tags: <fasta><sequence-annotation><genomics>
Title: Transfer annotations from one genome assembly to another
ThreadText: # Transfer annotations from one genome assembly to another
  
  (Asked by: username_0 on 2021-09-02)
  
  I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length assemblies. How do I annotate the output .fasta from the optical mapping assembly using the .gff of the draft assembly that was used as input? I also have a .agp file that describes what sequence fragments ended up where in the output.
  
  **Tags:** fasta, sequence-annotation, genomics
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-09-02. Score: 2
  
  You should use a liftover approach. You could either do this based on exact changes, which might be a bit tedious given the presumably large number of join operations you've done (especially if you've e.g. broken contigs).
  
  Therefore it might be more convenient to do it on the basis of homology.
  
  [liftoff](https://github.com/agshumate/Liftoff) is one simple tool for doing this with a gff file and your 2 fasta files. It seems to mostly work ok.
  
  
  ---
  
  