Running Deblur on paired-end sequences

[microbiomeAnalyst]

Hello, This is my first posting to the qiime forum. I’m using qiime2 version 2018.2.

I have paired-end reads and would like to try to denoise my illumina sequences using deblur. Does the deblur method (provided in the moving pictures tutorial) only work after forward and reverse sequences have already been merged as well as after primers/adapters ,have been removed?

• Can the trim length be defined for forward as well as reverse sequences (i.e. --p-trim-left-f 17, --p-trim-left-r 21)?

• It appears I can use the cutadapt method to remove the primers prior to running deblur?

• What is the best qiime2 command to merge the sequences prior to deblur, if necessary?

qiime deblur denoise-16S
–i-demultiplexed-seqs demux-filtered.qza
–p-trim-length 120
–o-representative-sequences rep-seqs-deblur.qza
–o-table table-deblur.qza
–p-sample-stats
–o-stats deblur-stats.qza

[wasade (Daniel McDonald)]

Hi @microbiomeAnalyst,

I apologize for the delayed response. Deblur is agnostic to paired or unpaired data. If you’d like to run paired data, then the reads will need to be joined prior to execution (for example, with qiime vsearch join-pairs), and because of this, any trim specific to fwd or rev would need to be done prior to execution. Deblur will remove adapters and PhiX. Cutadapt should be fine to execute prior to Delbur.

I hope that helps!

Best,
Daniel