Import demultiplexed paired-end reads into qiime


I am using the latest version of qiime and I have paired-end demultiplexed reads. I have folders for each barcode combination and for the forward and reverse reads.

I have noticed earlier posts about these topics but they used earlier versions of qiime.

Just wondering how I can import this data into qiime and commence merging/quality filtering using the DADA2 plugin.


Hi @Ilha_Byrne,

I would recommend the manifest format, which I think has been recommended over and over again on this forum. (Typically, if you’re not sure if things have changed, you can always check the change log!) The core plugins, especially importing, are pretty stable and usually forward compatible.


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