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Old 10-07-2010, 06:33 AM   #6
Location: Sweden

Join Date: Nov 2009
Posts: 83

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.
I have shotgun 454, paired end 454 and a range of paired end Illumina libraries as well as a mate pair library. I haven't yet found an assembler that can take all of the data for a hybrid assembly on any machine that I have access to. Velvet and Mira both take both types of data but have huge RAM requirements and are simply impractical to run. For hybrid cereal assemblies, what software are you using?
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