Homology guided assembly software

CImbusch

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Join Date: Oct 2009

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Homology guided assembly software

02-02-2010, 04:35 AM

Dear all,

I'm looking for a specific reference guided assembler. I had a look at

Software packages for next gen sequence analysis - SEQanswers

http://seqanswers.com/forums/showthread.php?t=43

Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

and there a plenty given. What I was wandering about is how closely related do those reference sequences have to be? For example I'm using MIRA and the backbone has to be very similar to the input reads for the assembly.

Is there maybe an assembler which can take a sequence from another species as a reference as to guide the assembly?
Is Mosaik capable of doing so?

Thanks in advance,
Charles
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