[mira_talk] Re: Merging contigs with mate-pair data ...
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 25 Aug 2009 09:09:44 +0200
On Mon, Aug 24, 2009 at 9:47 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Montag 24 August 2009 Martin A. Hansen wrote:
> > It surprises me that MIRA does not stitch - are you aware of any other
> > software that does?
>
> The only one I know (and that's because I was tolkd on this list) is phrap.
> But phrap doesn't know Solexa and I'm not sure how good it is with 454.
>
I shall try and post the question to Seqanswers.
>
> > 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).
>
> What's the available RAM on your machine?
>
I have 16Gb at my disposal, but not for several days at a time (a week end
run would probably be OK) ...
I will get something with 250Gb later in the year/early next year ...
> > Can I use the assembled 454 contigs
> > as really really long sanger reads in a de-novo assembly?
>
> No, only up to 20kb. Sorry.
>
Gawd, that's a shame - that would have been a work-around.
>
> > 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/
>
> Selecting contigs is done with "convert_project":
> convert_project -f caf -t caf -x 500 -y 20 input.caf output
> will, e.g., select all contigs with length >= 500 and average coverage >=20
> and write them to a new CAF. Veeeery useful to get cruft out of a project.
>
Is there a way to determine which reads ended up in the cruft and substract
them from another denovo-run?
I am trying a full denove assembly with:
mira -project=M1 -job=denovo,genome,normal,454,solexa
-GENERAL:number_of_threads=8 SOLEXA_SETTINGS -CO:msr=no
-GE:uti=no:tismin=2000:tismax=3000
I hope that looks allright. It looks like I am entering uncharted territory:
http://chevreux.org/uploads/media/mira3_solexadev.html#section_26
Best regards,
Martin
> Regards,
> Bastien
>
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