Re: [AMOS-help] about tigger in minimus2 pipeline

[Daniel S. <ds...@um...>]

Normally, the first step of minimus2, which is mummer, is limited to 5 GB of
sequence.  If you got passed the first step(mummer) then tigger memory usage
is determined by the edges in the assembly graph.  The edges in the graph
represent overlaps or alignments between the contigs.  So tigger can handle
millions of contigs if they don't share a bunch of overlaps in common.  If
your data is very repetitive you will need a large memory machine to run
tigger on millions of contigs.  Can you see if tigger is using all the
memory on the machine?

Dan


On Tue, Mar 15, 2011 at 4:41 PM, Ba, Hengxing <
Hen...@ag...> wrote:

>  HI
>
>   graph
>
> I think that no contigs could overlap in any one dataset. We assembly two
> same mammalian species with  different reads sets (solid and illumina) and
> different tools .
>
>
>
> I think it is good solution to merge two datasets.
>
>
>
> How much contigs in one dataset is acceptable to miminus2?
>
>
>
> Hengxing
>
>
>
>
>
> *From:* Daniel Sommer [mailto:ds...@um...]
> *Sent:* Wednesday, 16 March 2011 5:01 a.m.
>
> *To:* Ba, Hengxing
> *Cc:* amo...@li...
> *Subject:* Re: [AMOS-help] about tigger in minimus2 pipeline
>
>
>
> Why do you have so many contigs?   If they are all only  couple thousand
> base pairs you could just assemble them like they are sanger reads.
>
> Daniel Sommer
>
> On Mon, Mar 14, 2011 at 11:52 PM, Ba, Hengxing <
> Hen...@ag...> wrote:
>
> Thanks
>
> All these are contigs and no reads.
>
>
>
> Could you tell me how to merge two large contigs sets like mine?
>
>
>
> Hengxing
>
>
>
>
>
> *From:* Dan Sommer [mailto:dds...@gm...]
> *Sent:* Tuesday, 15 March 2011 4:42 p.m.
> *To:* Ba, Hengxing
> *Cc:* amo...@li...
> *Subject:* Re: [AMOS-help] about tigger in minimus2 pipeline
>
>
>
> No minimus2 can not handle millions of contigs.   Are these all contigs or
> are you including singleton reads?
>
>
>
> Daniel
>
> Sent from my iPad
>
>
> On Mar 14, 2011, at 7:45 PM, "Ba, Hengxing" <Hen...@ag...>
> wrote:
>
>  Hi
>
>
>
> Anyone could help me?
>
>
>
> I am running minimus2 pipeline to merge two large contigs sets. But the
> Tigger in pipeline has run 10 days and don’t finish yet.
>
>
>
> One contig set include 2376372 contigs and another  includes 1942129
> contigs.
>
>
>
> I wonder if it is difficult for Tigger to handle large datasets.
>
>
>
> Thanks
>
>
>
> Hengxing
>
>
>
>
>
>
>
>
>
>
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