As a new user interested in 16S rRNA gene sequence analysis with mothur, I need to understand the main stages of the MiSeq SOP workflow. Please outline the primary sections of the workflow from raw data processing to final analysis. Additionally, identify any commonly used 16S rRNA gene reference databases explicitly mentioned or linked within this SOP.
Navigate to 'https://mothur.org/wiki/'. Click on the 'MiSeq SOP' link (ID 32) in the navigation menu. Read through the MiSeq SOP page, paying attention to the major section headings that delineate the workflow stages. Identify and list the main workflow stages for 16S rRNA gene sequence analysis. Scan the entire page content for explicit mentions or direct links to common 16S rRNA gene reference databases like SILVA or RDP. Summarize the main workflow stages and state which reference databases are mentioned on the page.
The agent successfully navigates to the 'MiSeq SOP' page. The agent identifies and lists the main workflow stages, including (but not limited to): 'Getting started', 'Reducing sequencing and PCR errors', 'Processing improved sequences', 'Assessing error rates', 'Preparing for analysis', and 'Analysis'. The agent explicitly states that SILVA and RDP (or Greengenes) reference databases are mentioned on the MiSeq SOP page.