NovaSeq data in QIIME2

[AnkeWigger (Anke)]

Hello,

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 (https://github.com/benjjneb/dada2/issues/791).

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.

[lizgehret]

Hi @AnkeWigger,

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

@AnkeWigger

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 (Consequences of using dada2 on NovaSeq data · Issue #791 · benjjneb/dada2 · GitHub).

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.

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