NovaSeq data in QIIME2


I am new to bioinformatics and qiime2. For my research project I am doing a microbiome analysis in chickens. We want to send our samples to a sequencing company that uses novaseq6000. Although I have just learned how to import data into qiime2 (using the tutorials), I read the forum about complications of using novaseq data with qiime2 (

I know my data will be delivered in FASTQ format, but I assume I will thus also get this problem when trying to perform the quality analysis.

Can anyone inform me how to import the NovaSeq data into QIIME2 so that I can perform a quality control before studying the microbiota composition?

Thank you in advance.

Hi @AnkeWigger,

Thanks for reaching out! Happy to provide some suggestions below:

As discussed in this forum post, you have a few options here:

  • Use the dada2 R package with modifications as described by the Github link you shared above.
  • Use the dada2 R package or q2-dada2 as it is, since there are several reports without any significant variations between using Dada2 as it is (R or Qiime2) and the modified version.
  • Use Deblur which is not affected by changes in quality score binning.

Hopefully one of these options is a good solution for you!

Cheers :qiime2: :lizard:

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