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Old 12-29-2009, 01:07 PM   #3
Junior Member
Location: Amsterdam, Academic Medical Center

Join Date: Nov 2009
Posts: 6

Thanx for your reply!

What kind of artefacts would you expect to be produced? As far as I know how the Roche Reference Mapper works, I assume it uses a reference sequence/genome just a "guide" by witch a read is mapped to. The reference will not be involved in any base calls, nor will it be responsible for the erroneously joining of 2 genomic regions that should not be joined. I would expect that if one (set of) read maps to 2 distinct genomic regions in the reference genome, the contig will just stop at that part and this region will be a contig boundary. It is exactly this region that will be correctly assembled in a de novo approach. Hence my suggestion of combining both assembly methods in the assembly of highly divergent genomes.

Mauve is a great tool indeed (use it all the time)... Very candy-like pictures! I will look into the other one you suggested!

JurgenP is offline   Reply With Quote