[mira_talk] Re: High coverage data set, RAM limitations, subsampling.

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 10 May 2013 18:13:21 +0200

On May 10, 2013, at 18:02 , Felipe Gajardo <felipe.gajardo.e@xxxxxxxxx> wrote:
> $ mira --project=B0P1-8 --job=denovo,genome,accurate,iontor --notraceinfo

This is a 3.4.x version of MIRA. I highly recommend you use the current 
development version from SourceForge:
  https://sourceforge.net/projects/mira-assembler/files/MIRA/development/

> Is there a way to include the reads i left out of the assemble to complete it 
> (considering my RAM limitations)?

No, sorry. And you wouldn't want it neither as I suspect the additional 
coverage would introduce more consensus problems than it would reduce contigs. 
For 454 or Ion Torrent, 60x to 80x coverage should really not be exceeded.

> Does know MIRA that some reads are mate-paired if not having the traceinfo 
> file?

Yes, traceinfo file is not used for that. Read-naming is important.

> Could be a better approach make an assembly of a subset including exclusively 
> reads from the fragments library and after that, use the mate-paired 
> information to give order to the contigs obtained?

No. The pairs do help to build larger contigs, use them in the assembly.


Oh, and find yourself a computer with more RAM (sorry ;-)

B.
--
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts:

  1. Home
  2. mira_talk
  3. Archive
  4. 05-2013