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Old 12-18-2009, 03:21 AM   #1
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Location: Amsterdam, Academic Medical Center

Join Date: Nov 2009
Posts: 6
Cool Create the best prokaryotic genome assembly: Combining different methods

I use 454 titanium reads for my prokaryotic (bacterial) whole genome sequencing. The bacteria I am working on is highly diverse from strain to strain, with the gene content differing up to 15%. Therefore there are arguments to think of my project as a de novo sequence approach or a re-sequencing approach.

Doing a de novo assembly with the Newbler assembler, contig borders are in other parts of the genome then contig borders from the Refmapping software from Roche. So I would like to use the results from one assembly method in region A of my genome, and the results from the other assembly in region B of my genome. I would like to develop a strategy where I can combine these assembly methods.

Does anyone have an idea or an opinion on my approach?

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