How to create a manifest file using command line?

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??

Hi @SAHIL_JAIN_16110144,

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.


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 :smile:

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!


Thanks! @Micro_Biologist and @Mehrbod_Estaki for your help and support!


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