Microbiome Analysis

  1. Bioinformatics Data Processing
    1. Raw Data Handling
      1. File Format Understanding
        1. FASTQ Format Structure
          1. Quality Score Encoding
            1. Sequence Identifiers
            2. Data Storage and Management
              1. File Organization
                1. Backup Strategies
                  1. Version Control
                2. Initial Quality Assessment
                  1. Quality Control Tools
                    1. FastQC Analysis
                      1. MultiQC Reporting
                        1. Per-Base Quality Scores
                          1. Sequence Length Distribution
                            1. GC Content Analysis
                            2. Quality Metrics Interpretation
                              1. Phred Score Understanding
                                1. Quality Thresholds
                                  1. Problematic Patterns
                                2. Read Processing and Filtering
                                  1. Adapter Removal
                                    1. Adapter Identification
                                      1. Trimming Tools
                                        1. Parameter Optimization
                                        2. Quality Trimming
                                          1. Sliding Window Approach
                                            1. Quality Thresholds
                                              1. Length Filtering
                                              2. Contamination Removal
                                                1. Host DNA Removal
                                                  1. Vector Contamination
                                                    1. Cross-Contamination Detection
                                                  2. Paired-End Read Processing
                                                    1. Read Merging
                                                      1. Overlap Requirements
                                                        1. Merging Algorithms
                                                          1. Quality Score Handling
                                                          2. Read Pairing Validation
                                                          3. Error Correction and Artifact Removal
                                                            1. Chimera Detection
                                                              1. Chimera Formation Mechanisms
                                                                1. Detection Algorithms
                                                                  1. Removal Strategies
                                                                  2. Sequencing Error Correction
                                                                    1. Error Models
                                                                      1. Correction Algorithms
                                                                        1. Quality Improvement

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                                                                    5. High-Throughput Sequencing Technologies

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                                                                    7. Taxonomic Analysis and Profiling