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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
Thanks
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Hi,
did you solve the problem? right now, I have to solve the same problem. -
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-r42Comment
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