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Old 04-24-2013, 01:49 PM   #1
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Default create scaffold file from contig file and agp file?

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

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Old 05-10-2016, 01:32 AM   #2
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did you solve the problem? right now, I have to solve the same problem.
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Old 05-10-2016, 02:53 AM   #3
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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:

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