Regarding the Installation and analysis of shot gun metagenomics samples

Respected members of the forum
I am new to this forum, and I need help with the installation and analysis of shotgun metagenomic samples to identify the taxonomy, functional genes, anti-biotic resistance genes, and pathways.
Thanks in advance.
Best Regards

The tasks you’re describing can be performed with MetaPhlAn and HUMAnN. You can find introductions to those (and other) methods via the tiles here:

Hi @ Franzosa
Thanks for your reply.
I want to know how to input paired-end multiple files.
Can you please give an example here.
thanks and Regards

You can see here for an intro about working with paired end files during QC with KneadData:

After that, most of our tools just concatenate all the surviving reads into a single file of single-end reads for analysis.