Concatenate unpaired reads R1 R2


I am trying to concatenate forward and reverse reads that DO NOT overlap. I am not clear if the ‘qiime feature-table merge-seqs’ function is doing this (attached my code below). Please confirm if this is the case. Is there a way to add 10 Ns between R1 and R2?

I appreciate your help,


qiime feature-table merge-seqs **
–i-data rep-seqs-dada2AMFEC_R1QIIME.qza **
–i-data rep-seqs-dada2AMFEC_R2QIIME.qza **
–o-merged-data rep-seqs-dada2AMFEC_R1R2mergedQIIME.qza

Hi @camzdel,
Currently there is no way to merge non-overlapping reads in Qiime2. This is often not a recommended way to handle paired-reads so I’m not sure if this will even be a supported function any time soon. For this you’ll have to look for a tool outside of qiime2, and unfortunately I don’t have any experience with this to give any recommendations either. Perhaps others can comment.
The merge-seqs isn’t used for merging reads in the way you’re thinking, but instead its used for combining some separate sequences, say from a few different runs, into one artifact.

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