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Old 09-04-2017, 10:59 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,992

Provided your primers have covered the gene fully you could assemble the reads (after merging the pairs post demultiplexing/removal of barcodes).

Should be easy enough to test. Use (for merging the reads) and to assemble the data. Using (for trimming) would be optional in case you have adapter contamination in your data. All tools part of BBMap suite. They all have individual threads.
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