[mira_talk] Re: megahubs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 Jun 2014 21:08:59 +0200
On 25 Jun 2014, at 16:34 , Jose Huguet Tapia <jch63@xxxxxxxxxxx> wrote:
> I am using MIRA 4 to assembly an Oomycete (Eukaryotic). I believe that the
> organism has a highly heterozygous genome.
One warning: a few weeks ago I’ve had the unpleasant surprise to discover that
the HGAP3 pipeline totally fails to give reliable corrected reads for a diploid
genome. It simply mixed differences fromdifferent ploidies into single reads.
Of course assemblers which recognise this barf and will create many more
contigs than you’d expect (MIRA certainly does, the one from the HGAP pipeline
also).
> I run a "first test" in MIRA with Pacbio corrected Long reads. The assembly
> was going ok until I got the message of megahubs. From previous discussion I
> learned that megahubs are quite common in eukarotycs.
> My concern is the level of total megahubs . It is more than 90 %.
Errrm, yes. 99% megahubs points to a hefty problem. I know that MIRA 4.0.2 has
some trouble correctly defining megahubs for long read data, but 99% is just
ridiculous. Something feels fishy, either regarding MIRA or the data.
> In the message It says that I set the a maxium allowed ratio of 90. I believe
> that I did not set this parameter though. Does MIRA 4 have a default for this.
Yes, MIRA sets default according to the data you feed it. Am I correct in
assuming you used a pretty standard manifest to launch this assembly?
B.
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