[mira_talk] Re: suggestion to trim contaminants before assembly process
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 3 Dec 2009 20:58:40 +0100
On Donnerstag 03 Dezember 2009 Laurent MANCHON wrote:
> Lucy is a good tool but not easy to configure and you need to make
> several tests changing each time parameters to obtain good results,
> the major advantage of SeqTrim is the facility to configure and the
> connectivity with others processing tools particularly with RepeatMaskers.
> For more documentation and to compare with other tools i would suggest
> to read paper here: http://www.springerlink.com/content/r03453727548t69h/
Interesting how things coincide: bevause of a request I've rewritten just
yesterday the SSAHA parsing code to now read SSAHA2 results and tried it out
on some test data I have. Boy, have I been impressed how well that works to
trim away sequencing vectors. In many Sanger assembly cases MIRA now just
needs the sequence, quality and the SSAHA2 vector screening info. And it's
really easy to use.
If anyones's interested to have a look at it before version 3 (look for
'ssaha' in the main manual as well as the quick walkthrough in the usage
manual):
http://www.chevreux.org/tmp/mira_3rc4d_dev_linux-gnu_x86_64_static.tar.bz2
Regards,
Bastien
PS: but I put SeqTrim back on the 'have a look at it when there's time' list
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