Microbiome Analysis

  1. High-Throughput Sequencing Technologies
    1. Amplicon Sequencing Approaches
      1. Target Gene Selection
        1. 16S rRNA Gene
          1. Bacterial Identification
            1. Hypervariable Regions
              1. Primer Selection
              2. 18S rRNA Gene
                1. Eukaryotic Identification
                  1. Primer Design
                  2. Internal Transcribed Spacer
                    1. Fungal Identification
                      1. ITS1 vs ITS2 Regions
                      2. Functional Genes
                        1. Nitrogen Cycling Genes
                          1. Carbon Cycling Genes
                        2. PCR Amplification Strategies
                          1. Primer Design Principles
                            1. Degenerate Primer Use
                              1. PCR Optimization
                                1. Bias Minimization
                                  1. Amplification Conditions
                                  2. Library Preparation
                                    1. Indexing Strategies
                                      1. Barcode Design
                                        1. Adapter Ligation
                                          1. Size Selection
                                            1. Quality Control
                                          2. Shotgun Metagenomic Sequencing
                                            1. Whole Genome Approach Advantages
                                              1. Taxonomic Resolution
                                                1. Functional Profiling
                                                  1. Novel Gene Discovery
                                                  2. DNA Fragmentation Methods
                                                    1. Mechanical Shearing
                                                      1. Enzymatic Fragmentation
                                                        1. Fragment Size Control
                                                        2. Library Construction
                                                          1. End Repair
                                                            1. A-Tailing
                                                              1. Adapter Ligation
                                                                1. Size Selection
                                                                  1. Amplification
                                                                  2. Sequencing Platform Selection
                                                                    1. Short-Read Technologies
                                                                      1. Long-Read Technologies
                                                                        1. Hybrid Approaches
                                                                      2. Metatranscriptomic Sequencing
                                                                        1. RNA-Seq Principles
                                                                          1. mRNA Enrichment
                                                                            1. rRNA Depletion
                                                                              1. cDNA Synthesis
                                                                                1. Library Preparation
                                                                                  1. Sequencing Considerations
                                                                                  2. Sequencing Platform Technologies
                                                                                    1. Illumina Sequencing
                                                                                      1. Sequencing by Synthesis
                                                                                        1. Paired-End Sequencing
                                                                                          1. Read Length Options
                                                                                          2. PacBio Sequencing
                                                                                            1. Single Molecule Real-Time
                                                                                              1. Circular Consensus Sequencing
                                                                                                1. Long-Read Advantages
                                                                                                2. Oxford Nanopore Sequencing
                                                                                                  1. Nanopore Technology
                                                                                                    1. Real-Time Sequencing
                                                                                                      1. Ultra-Long Reads
                                                                                                      2. Platform Comparison
                                                                                                        1. Throughput Considerations
                                                                                                          1. Accuracy Differences
                                                                                                            1. Cost Analysis
                                                                                                              1. Application Suitability

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                                                                                                          4. Nucleic Acid Extraction and Quality Assessment

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                                                                                                          6. Bioinformatics Data Processing