[mira_talk] Re: Assemble 454 contigs and Sanger reads
- From: Cleo HC Ho <cleoho175@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 22 Nov 2010 10:08:03 -0500
Thank you, Peter, for the response. But I've already done a hybrid assembly
with 454 reads and Sanger reads. And now I'm trying to assemble the 454
contigs and the Sanger reads to see if it improves the assembly.
Mainly I'm trying to figure out how to run this latter trial. Again, since
MIRA does not output an XML file for the 454 contigs, should I load the 454
contigs into MIRA without the XML? Or this idea of assembling 454 contigs
and Sanger reads simply isn't feasible in MIRA?
Thanks.
On Mon, Nov 22, 2010 at 4:58 AM, Peter <peter@xxxxxxxxxxxxxxxxxxxxx> wrote:
> On Mon, Nov 22, 2010 at 9:11 AM, Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
> wrote:
> > On Mon, Nov 22, 2010 at 1:01 AM, Cleo HC Ho <cleoho175@xxxxxxxxx> wrote:
> >> Hi all,
> >>
> >> I am trying to assemble 454 contigs (already produced by MIRA) and some
> >> Sanger reads as a hybrid assembly in MIRA.
> >>
> >> This task inevitably leads to my question: since MIRA does not output an
> XML
> >> file for my 454 contigs, how can I run this hybrid assembly? Should I
> load
> >> my 454 contigs into MIRA without the XML? Or this idea of assembling 454
> >> contigs and Sanger reads simply isn't feasible in MIRA?
> >>
> >> Thanks.
> >> Cleo
> >
> > You could do a hybrid assembly of the 454 reads and the Sanger reads,
> > MIRA is happy with that. If it isn't too computationally demanding, I
> would
> > try this first.
> >
> > Alternatively you could try treating the 454 contigs (with their quality
> scores)
> > as Sanger reads, but if they are too long you may need to shred them...
>
> It occurred to me later to suggest that you might want to try using a
> classic
> assembly tool like PHRAP to combine 454 contigs and capillary reads, but
> you have already tried that:
> http://seqanswers.com/forums/showthread.php?t=7990
>
> Peter
>
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