Generating Taxonomy and Sequence References for Microbial Functional Genes Using Qiime2.
Hi all, As you know, analyzing 16S (housekeeping gene) sequence by Qiime2 is required to provide taxonomy and sequence references. We can find them in the SILVA database. I essentially need taxonomy and sequence references for analyzing my functional genes data to go through the downstream processes. To generate them, what I was told, one should apply from NCBI website tools, such as FTP, e-utility and e-fetch, which my knowledge in this area is sadly rudimentary. I need your assistance to give me an in-detailed protocol to generate them. I am looking forward to hearing from you. Thanks a lot.
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Probably this paper will help a lot:
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses