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Old 02-10-2017, 08:28 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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You could try a reference guided assembly, perhaps using MIRA?

You might want to first try mapping all the reads against the reference (with relaxed mapping settings) in order to divide the reads into those which might be part of your virus (mapped to the reference) or not (unmapped).
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