SEQanswers - View Single Post - Create the best prokaryotic genome assembly: Combining different methods

flxlex · 12-29-2009, 07:11 AM

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: http://bioinformatics.biol.rug.nl/we...tor2_start.php).

flxlex

12-29-2009, 07:11 AM	#2
flxlex Moderator 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: http://bioinformatics.biol.rug.nl/we...tor2_start.php). flxlex