[mira_talk] Re: megahubs
- From: Jose Huguet Tapia <jch63@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 Jun 2014 15:48:55 -0400
Bastien,
I used a very simple manifest for this first test.
project=Pythium_mira_pacbio
job =genome,denovo,accurate
parameters = COMMON_SETTINGS -GE:not=4
readgroup = pythiumPACBIO
data = corrected_LR.fastq
technology = PcBioLQ
On Wed, Jun 25, 2014 at 3:08 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> 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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