[mira_talk] Re: Merging contigs with mate-pair data ...
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 24 Aug 2009 20:41:21 +0200
Hello Bastien and welcome back.
It surprises me that MIRA does not stitch - are you aware of any other
software that does? I shall try MIRA with a full de-novo assembly - but I
fear the memory consumption (I may try to sample a few hundred thousands of
the Solexa reads to limit the memory consumption, and hope that there is
enough information to close the gaps). Can I use the assembled 454 contigs
as really really long sanger reads in a de-novo assembly?
The reason why I used the FASTA entries was so that I could easily select
contigs above 500 bp in length (there is no switch for that as far as I can
tell?). I didnt want MIRA stitching together the smaller - probably
non-sense - stuff. Well, that was not a problem since there was no stiching
at all :o/
Martin
On Mon, Aug 24, 2009 at 8:31 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Freitag 21 August 2009 Martin A. Hansen wrote:
> > [...]
> > However, I still get the same number of contigs - am I doing something
> > wrong?
>
> Hello Martin,
>
> sorry, was away for some days else I'd have responded earlier.
>
> Nothing wrong per se, it's just that MIRA will not assemble backbones
> together, or stitch them together with new sequences that would bridge the
> gap.
>
> The *only* sensible way to use the Solexas at the moment is to use them
> together with the 454s in a de-novo assembly:
> "--project=M1 --job=denovo,genome,accurate,454,solexa" ... + other options
>
> One more remark: you used the FASTAs of the 454 de-novo assembly as
> backbone.
> With this you loose all the information contained in the alignment of the
> 454
> sequences. I recommend using CAFs in those cases, they contain everything.
>
> Regards,
> Bastien
>
>
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