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Old 11-20-2013, 06:50 AM   #8
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Location: San Francisco

Join Date: Aug 2012
Posts: 322

+1 for Cerulean, I have seen some really good results for small assemblies and it is computationally efficient.
Another option for a small genomes, even if you don't have enough coverage to get great denovo PacBio results, HGAP you will still give reasonable sized assemblies with 35-40x coverage, just very fragmented. You could assemble everything independently and merge the assemblies with something like minimus2.
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