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

Question

[Michael R. Crusoe]

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?

Answer 1

[Pierre Lindenbaum]

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

[Michael R. Crusoe]

This looks like a winner; thanks!

[Michael R. Crusoe]

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.