[mira_talk] Re: CNAG
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 25 Mar 2011 19:47:22 +0000
On 25/03/11 17:45, Bastien Chevreux wrote:
On Thursday 24 March 2011 13:17:04 Tony Travis wrote:
> Has anyone submitted a MIRA assembly to:
> http://cnag.bsc.es/
Both the dataset used by dnGASP as well as the Assemblathon are way out
of the scope of MIRA. E.g., 1.8 gigabase organism at 44x coverage with
reads of 114bp for example is something like 800m reads. Definitively
not possible with MIRA.
I'll continue to concentrate now on the range of 50m to perhaps 100m
reads ... and do that one right :-)
Hi, Bastien.
OK, how about attempting to assemble the smaller 'large' insert
libraries with MIRA, and then mapping the 500bp reads onto that?
cov length and type genomic orientation and insert size
44x 2 x 114nt paired-end --> 500bp <--
8x 2 x 36nt mate-pair <-- 3kb -->
8x 2 x 36nt mate-pair <-- 5kb -->
4x 2 x 36nt mate-pair <-- 10kb -->
Just a thought...
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk
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