[mira_talk] Re: Vector screen
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Mar 2011 11:14:19 +0000
On 16/03/11 08:31, Jose Blanca wrote:
Hi:
We usually clean the reads before doing a Mira assembly. We have created
a pipeline to do that. You can take a look at:
http://bioinf.comav.upv.es/ngs_backbone/
If you'd like to try it out, I'd recommend to use the latest code,
because recently we have been refactoring the cleaning code.
https://github.com/JoseBlanca/franklin
Also, we're very interested in this cleaning process right now, so if
someone has some suggestion we would be very pleased to consider adding
it to out pipeline.
Hi, Jose.
That looks interesting!
I used to use "cross_match" from the Phed/Phrap pipeline, but recently
decided to start using "ssaha2" instead after reading about other people
using it on the MIRA list. It seems to work quite well, but I'm
interested in trying out your pipeline on our Beowulf cluster here.
Thanks,
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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