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.