Oxford Nanopore sequencing

Hi all,

I have a demultiplexed data from Minion Mk1b sequencer. I was able to import the data into Qiime (the latest version) and trim the data. However, when I try to use DADA2 for denoising I am getting the below error (attached pictures). I looked Qiime forum and it looks like we cannot use Qiime for sequence data from the Nanopore sequencer. I was wondering if this is still the case. Moreover, I have some sequences with larger than my target (V3-V4; 570bp), could this be primer dimer or chimera sequence? I blasted some of those sequences and for example one of them has 94% similarity with Ecoli plasmid.

Hi, Javad
DADA2 is inappropriate for Nanopore long reads: Nanopore variable region sequencing analysis · Issue #1364 · benjjneb/dada2 · GitHub
QIIME2 does not have preprocessing methods for ONT.



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