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

Join Date: Feb 2008
Posts: 6,992
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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 bbmerge.sh (for merging the reads) and tadpole.sh/seal.sh to assemble the data. Using bbduk.sh (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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