[Bioperl-l] Split ACE file by AGP scaffolds

Nathan Watson-Haigh nathan.watson-haigh at awri.com.au
Wed Jan 11 01:42:30 EST 2012

I have an ACE file (500k contigs > 500bp) generated by Newbler for a 450MB genome which I'd like to open in consed. However, due to its size and my computer memory limits it only opens 10-15%.

I'm trying to spilt the ACE file into smaller subsets of contigs which i can handle in consed.

I think a valid approach is to generate an ACE file per scaffold and work in consed on each scaffold in turn. Does this sound valid?

If i take the AGP file that Newbler generated, i should be ankle to take the monolithic ACE file and split it into 20k ACE files representing each scaffold.

Does anyone have thoughts on whether this is doable with the BioPerl with the Bio::Assembly:IO:ace module? If so, could you give me a couple of quick pointer?

Cheers, Nath

Sent from my Android phone.

Nathan Watson-Haigh
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