Can I use QIIME2 for my metagenomes?

Hello everyone :slight_smile:

I am a new QIIME2 user (read: relatively new to bioinformatics/coding all together) and I am wondering if QIIME2 would be right for my investigations. I am running through the online tutorials and these all include primer and barcode data.

I have 1 sample of purified DNA from an undescribed, microbial soil community. I have not amplified anything, and as such I have no primers. I also have no barcodes for these, or really anything else than just T’s C’s G’s & A’s… One forward read, and one reverse read, each about 1GB.

I want to ID the species, and any already described genes in my sample. Then hopefully compare changes to these communities, and functional networks across different seasons throughout the year.

Will QIIME2 allow me to do this without primer and barcode data?

Thank you so much for any help,

Hi @Rodrigo.ZG,
Thanks for getting in touch about this. At the moment, the sequence annotation functionality available in QIIME 2 is exclusively for marker gene amplicon data, though we are working with some teams to develop plugins for shotgun metagenome analysis and annotation (which sounds like what you need). So, QIIME 2 probably won’t get you want you want right now. I would recommend taking a look at the Biobakery tools. A lot of these will be available as QIIME 2 plugins in the future, but for now you should just use them directly.

Hope this helps!

Thank you for such a quick reply, and for the suggestion! :slight_smile:

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