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Old 10-08-2013, 06:00 AM   #3
Location: haifa israel

Join Date: Jun 2011
Posts: 62

Sorry for the confusion!
We have a WGS metagenome; ignore the word amplicon here. I think they somehow tried to select for short fragments when the prepared the library but I will double check on this. (ie, not sure whether this means the 100bp PE is overlapping or no). Like I said- new to metagenomes....

Any suggestions as to the best programs to use for ref-guided assembly? Although I have about 50 homologues of the gene and I am not really sure which to choose.

Thanks for your advice!
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