create scaffold file from contig file and agp file?

[Wallysb01]

Does anyone know how to go from a contig file with the scaffolding information in an AGP file to a full scaffolded multifasta file?

Thanks

[aajosselin]

Hi,
did you solve the problem? right now, I have to solve the same problem.

[Markiyan]

If you have contigs with scaffolding info in the agp file -

Than you can pad gaps between the contigs with N's (according to agp file) and write a multifasta file with an entry for each scaffold. Can be done with a bit of perl programming.

(In my case I use newbler output, which includes the scaffolds sequences in the multifasta file).

If you have source reads data, and would like to try a different scaffolder(s) -

have a look at the following review for the scaffolding tools available:

https://genomebiology.biomedcentral....-2014-15-3-r42