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Old 08-02-2012, 07:21 AM   #1
mcastro
Junior Member
 
Location: Barcelona

Join Date: May 2011
Posts: 7
Default Viral genome assembly from RNA-seq data

Hi,

I'm performing a RNA-seq analysis from a virus infected plant. After mapping the Illumina Hiseq paired reads against the plant genome, I used the unmapped reads to blast the virus genome available. Once I separated virus reads from other unmapped reads I would like to assembly the virus genome. Which is the best way to do it? I used before velvet and trinity for eukaryote transcriptome assemblies but I'm not sure if I can use the same software or approach for virus.

I would appreciate someone could guide me.

Thanks a lot
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