[mira_talk] Re: Merging contigs with mate-pair data ...
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 24 Aug 2009 21:47:37 +0200
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 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?
> Can I use the assembled 454 contigs
> as really really long sanger reads in a de-novo assembly?
No, only up to 20kb. Sorry.
> 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.
Regards,
Bastien
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