software to link sequencing fragments

Simon Andrews simon.andrews at bbsrc.ac.uk
Thu Aug 2 04:54:00 EST 2001


"¡¡Ryan" wrote:
> 
> hi,all,
> 
> I want to find a software which can help me to link different sequencing
> fragments(forward and reverse) into a consensuse sequence. I have tried
> DNASIS 2.5. But it dosen`t work well.
> thank you very much.

>From my experience, the Staden package is excellent for this type of
work.  It works happily with either traces or plain sequence (though
traces are much more useful if you have the option).  It can also
integrate with Phred/Phrap if you need.

There are several modules to Staden (it also does sequence analysis),
but for assembly the ones you need are Pregap (for processing traces),
and Gap4 (for the actual assembly).

It's available for free to academics, on a wide range of platforms
(including Windows).  You can download it from;

	http://www.mrc-lmb.cam.ac.uk/pubseq/


Hope this helps

Simon.




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