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Old 10-07-2010, 05:40 AM   #5
jimmybee
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Location: Adelaide, Australia

Join Date: Sep 2010
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If its highly repetitive (my definition of highly would be >80%), then doing a 1x coverage run wouldn't be particularly effective, nor will it compliment the illumina data for the hybrid assembly. You'll need to figure out a few things like how finished do you want the sequence and what information do you want out of the assembly (eg. just good assembly of genes or repeats).

To answer natstreet: Hybrid assemblies with different types of data are the way to go for repetitive genomes (such as cereal crops). We've found that integrating differing types of data (paired end/fragment), different insert sizes and read lengths can been very beneficial to the assembly.
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