[mira_talk] Re: mira vs newbler
- From: Miguel Pinheiro <monsantopinheiro@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 17 Jan 2010 22:50:26 +0000
Hi,
I totality agree with your choice, because I tried to use the Newbler in EST
but the results were desapointing.
I also contacted Roche and uploaded the sff files for them to explain the
results.
The mira built several transcripts that newbler didn't form.
But I have some memory problems trying to assemble metagenomic data when
coming from non-normalize samples.
The mira consumes lots of memory, and crashes, because of the megahubs.
Of course, in the begining of assembler, the mira creates the warning
message of megahubs and suggests the change of parameters. But when I change
the parameters the memory isn't enought.
So, if you allow me, I have a suggestion... Is it possible to remove, for
example, half of reads in the fasta and fastq, that are present in megahubs,
to avoid their forming??? For example, if I remove the smaller reads that
are present in megahubs I avoid their formatation. This is not an analisys
of SNP detection, so I think there's no loss of information... This make
cense???
Miguel Pinheiro
On Fri, Jan 15, 2010 at 4:57 PM, Andrzej N <andrzej.k.n@xxxxxxxxx> wrote:
> I tried both MIRA and Newbler...I'm staying with MIRA :).
>
> Highly recomended!
>
> Andrzej
>
>
> On Fri, Jan 15, 2010 at 6:06 AM, Jose Blanca <jblanca@xxxxxxxxxx> wrote:
>
>> newbler --version
>>
>> newbler Software Release: 2.3-PreRelease-10/19/2009
>>
>>
>> On Friday 15 January 2010 12:11:12 Peter wrote:
>> > On Fri, Jan 15, 2010 at 9:42 AM, Jose Blanca <jblanca@xxxxxxxxxx>
>> wrote:
>> > > The latest (yet unreleased) one. I did it with the -cdna option. The
>> > > theory is very nice, because it returns "transcripts" (names isotigs)
>> and
>> > > "genes" (named isogroups), but the result is awful.
>> > > Regards,
>> > >
>> > > Jose Blanca
>> >
>> > Do you mean Newbler gsAssembler 2.3 which includes improved EST
>> > assembly (released at the end of last year I think)? Or something even
>> > newer?
>> >
>> > Peter
>>
>>
>>
>> --
>> Jose M. Blanca Postigo
>> Instituto Universitario de Conservacion y
>> Mejora de la Agrodiversidad Valenciana (COMAV)
>> Universidad Politecnica de Valencia (UPV)
>> Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
>> 46022 Valencia (SPAIN)
>> Tlf.:+34-96-3877000 (ext 88473)
>>
>> --
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>
>
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