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Old 12-29-2009, 07:11 AM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

I always feel refmapping is a bad idea, as you might get artifacts, and you should use the unmapped reads for de novo discovery of regions missing in the reference. So, I would assemble de novo and then use comparative tools to order your contigs, such as Mauve Contig Mover (http://bioinformatics.oxfordjournals...ull/25/16/2071) or Projector2 (not a big fan, but here is the site:

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