1 Overview of Mothur Pipeline Steps

1.1 Data Preprocessing

• Input Data: Understand the required format and structure of your sequencing data.
• Quality Control: Perform initial quality checks to filter out low-quality sequences.

1.2 Sequence Alignment

• Alignment Process: Align sequences to a reference database for further analysis.
• Reference Databases: Explore available reference databases for alignment.

1.3 Taxonomic Classification

• Assign Taxonomy: Identify the taxonomic origin of each sequence.

1.4 Diversity Analysis

• Alpha Diversity: Assess diversity within individual samples.
• Beta Diversity: Explore diversity between different samples.

1.5 Statistical Analysis

• Hypothesis Testing: Apply statistical tests to identify significant differences.
• Visualization: Create visualizations to interpret the results effectively.

1.6 Interpretation and Reporting

• Biological Insights: Derive meaningful biological interpretations from your analysis.
• Report Generation: Communicate your findings through reports or visualizations.