Manifest file for paired-end reads

[thermokarst]

@lmanchon

ok, i have imported all my demultiplexed paired-end files using manifest-file

Good!

@lmanchon

And now which command i need to run to link my metadata file with the raw data ?

No need, that isn't how metadata works in QIIME 2. Take a look at the Metadata tutorial for more info. Also, if you haven't gone through the Overview, please start there!