I am a new user of mothur and need to understand how to use it for 16S rRNA gene sequence analysis. Please navigate to the MiSeq SOP page within the Wiki, and identify the main steps involved in processing 16S rRNA gene sequences from raw data to final analysis. Also, locate any direct mentions or links to commonly used reference files (like SILVA or RDP) on this page.
Navigate to 'https://mothur.org/wiki/'. Click on the 'MiSeq SOP' link (ID 32) in the navigation menu. Read the introduction and main sections of the MiSeq SOP page to identify the primary steps for 16S rRNA gene sequence analysis. Scan the page content for any explicit mentions or direct links to common reference files such as SILVA or RDP. Summarize the main steps for 16S rRNA gene sequence analysis and state whether any direct links or prominent mentions of SILVA or RDP reference files were found on this specific page.
The agent successfully navigates to the 'MiSeq SOP' page. The agent identifies and lists the main steps of 16S rRNA gene sequence analysis as described on the page (e.g., quality control, alignment, chimera removal, classification, phylogenetics, diversity analysis). The agent explicitly states whether direct links or prominent mentions of SILVA or RDP reference files are found on the MiSeq SOP page itself.