How to process the fastq files from the NCBI SRA using qiime2?

Hi there,
I have been downloading the NCBI SRA fastq project files and most of them have fastq sequences per sample basis. However, in some of the project file submitted to the SRA (Gopalakrishnan et al 2018 Science, ), I find that there is a single project fastq file with big size (I am not sure but just guessing is it a single file with fastq files merged from all project samples?( link to the fastq file: SRA Archive: NCBI
This particular project has n=112 patient samples. Could you guys please suggest how can I process this fastq file through qc and dada2?

Hi @Man,

Have you tried the q2-fondue plugin?

If this works, you should be ready to go with any downstream processing, using the tutorials as a guide.

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