Shotgun sequence analysis

Hi @thermokarst I want to know can we analyze the raw shotgun/whole metagenome sequences with the help of the QIIME 2 pipeline? I would like to mention that I have 10 samples, each read (forward and reverse) contains about 8 GB of data.
eagerly waiting for your response

I'm not Thermokarst, but you could try the SHOGUN plugin for shotgun reads.

Full paper on SHOGUN: SHOGUN: a modular, accurate and scalable framework for microbiome quantification - PubMed
GitHub: GitHub - knights-lab/SHOGUN: SHallow shOtGUN profiler

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Last I checked, the SHOGUN plugin seemed like it needed some updates - it may or may not work at the moment, but you can find some documentation of it here.

While it won't help at the moment, there is a suite of plugins to support shotgun analysis in progress, so this may be ready to go for your next analysis. In the meantime, another option is that you can generate pathway/gene family/taxonomy tables with HUMANn and MetaPhlan, and import those tables for analysis with QIIME 2 using the new q2-sapienns plugin. I expect to put some documentation together on installing q2-sapienns in a QIIME 2 2022.8 environment in the next few days, and will post it to Community Contributions when I do.

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Thank you so much @gregcaporaso and @colinbrislawn for the kind support.