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Tool To Create Scaffold Fasta File From An Agp And Contig Fasta File?

We have an AGP file and its corresponding fasta file of contigs and we'd like to generate a fasta file of the scaffolds: that is one with the contigs separated by the appropriate number of Ns.

Any pointers?

fasta scaffolding contigs
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updated by corey.wischmeyer • corey.wischmeyer • written by Michael R. Crusoe Michael R. Crusoe

1 answer

Searching for AGP2fasta returns that perl code: https://github.com/WormBase/wormbase-pipeline/blob/master/for_cvs/agp2fasta.pl

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written by Pierre Lindenbaum Pierre Lindenbaum

Confirmed to work under Ubuntu with bioperl 1.6.901-2

Note: this script doesn't handle comment lines (those beginning with a '#') but that is easily remedied.

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written by Michael R. Crusoe Michael R. Crusoe

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