[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
Senior Bioinformatician  | The Australian Wine Research Institute
Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | Map
PO Box 197, Glen Osmond SA 5064, Australia
T: +61 8 83136836 (direct) | F: +61 8 83136601 |
www: www.awri.com.au | AWRI Events

This communication, including attachments, is intended only for the addressee(s) and contains information which might be confidential and/or the copyright of The Australian Wine Research Institute (AWRI) or a third party. If you are not the intended recipient of this communication please immediately delete and destroy all copies and contact the sender. If you are the intended recipient of this communication you should not copy, disclose or distribute any of the information contained herein without the consent of the AWRI and the sender. Any views expressed in this communication are those of the individual sender except where the sender specifically states them to be the views of the AWRI. No representation is made that this communication, including attachments, is free of viruses. Virus scanning is recommended and is the responsibility of the recipient.




More information about the Bioperl-l mailing list