I have a 100 fastq files (100 each for forward reads and reverse reads). I want to import these files into QIIME2. I need to create a manifest file for this purpose. Do I need to create the file manually or can it be done using some command??
Right now, you need to create the manifest yourself. If you write your own code, sometimes you can use python or bash to produce something manifest-like, but there's no automated way to do it right now.
Best,
Justine
Though I never tried this myself, there is at least one attempt at automating manifest making. See @Micro_Biologist's script here for example.
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It doesnt work right now... I've been busy with other projects but if anyone wants to fix it, it is 99% there!
It works fine just tested with the qiime2-2019.4 conda environment 
You'll have to install 'send2trash' (or make a minor edit to the code) to use in the qiime2 conda environment I ran this:
pip install send2trash
Hope it works okay!
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Thanks! @Micro_Biologist and @Mehrbod_Estaki for your help and support!
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