[mira_talk] Re: 0.5TB not enough space?
- From: Iddo Friedberg <idoerg@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Aug 2011 20:32:20 -0400
On Mon, Aug 15, 2011 at 2:01 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> **
>
> On Monday 15 August 2011 19:36:32 Iddo Friedberg wrote:
>
> > Oops. I put up the wrong logfile. The run was definitely not on an NFS
>
> > system
>
>
> Heavens! Is there any valid reason you set up an assembly with a coverage
> >= 1000x ? No, not ten, not one hundred ... one thousand! You are aware that
> this actually decreases the quality of a genome assembly, right? Non-random
> errors in the sequencing will be the death of it.
>
>
> You might want to read quickly through
>
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_seqadv_a_word_or_two_on_coverage
>
>
> especially the small paragraph labelled with a nice, warm and re-assuring
> "Warning".
>
>
> Back to your project: slash down the amount of data by a factor of ten and
> all will be well :-)
>
>
> B.
>
>
> PS: and I'm actually now thinking of adding another warning flag which will
> let MIRA stop if it detects a coverage >= 150x in genome de-novo ... anyone
> having an oppinion on this?
>
>
>
>
Seems like I should be the strongest supporter of this proposal ;)
--
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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