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• Introduction
  • The concept of CLC Microbial Genomics Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Microbial template workflows
  • Taxonomic Analysis template workflows
    • Data QC and Remove Background Reads
    • Data QC and Taxonomic Profiling
    • Merge and Estimate Alpha and Beta diversities
    • QC, Assemble and Bin Pangenomes
  • Amplicon-Based Analysis template workflows
    • Data QC and OTU Clustering
    • Detect Amplicon Sequence Variants and Assign Taxonomies
    • Estimate Alpha and Beta Diversities
  • Typing and Epidemiology template workflows
    • Compare Variants Across Samples
    • Create MLST Scheme with Sequence Types
    • Map to Specified Reference
    • Type Among Multiple Species
    • Type a Known Species
  • QIAseq Analysis template workflows
    • Analyze QIAseq xHYB Mycobacterium Tuberculosis Panel Data (Human host)
    • Analyze QIAseq xHYB Viral Panel Data (Human host)
    • Find QIAseq xHYB AMR Markers (Human host)
  • QIAseq Panel Analysis Assistant
• De Novo Assemble Metagenome
• Amplicon-Based Analysis
  • Normalize OTU Table by Copy Number
  • Filter Samples Based on Number of Reads
  • OTU clustering
    • OTU clustering parameters
    • OTU clustering outputs
    • Importing and exporting OTU abundance tables
  • Remove OTUs with Low Abundance
  • Align OTUs with MUSCLE
  • Detect Amplicon Sequence Variants
    • Detect Amplicon Sequence Variants parameters
    • Detect Amplicon Sequence Variants output
    • Importing ASV abundance tables
  • Classify Long Read Amplicons
    • Classify Long Read Amplicons parameters
    • Classify Long Read Amplicons output
• Taxonomic Analysis
  • Contig Binning
    • Bin Pangenomes by Taxonomy
    • The Taxonomy Binning Report
    • Bin Pangenomes by Sequence
  • Taxonomic Profiling
    • Taxonomic Profiling parameters
    • Taxonomic Profiling output
    • Taxonomic Profiling abundance table
  • Identify Viral Integration Sites
    • The Viral Integration Viewer
    • The Viral Integration Report
• Abundance Analysis
  • Merge Abundance Tables
  • Refine Abundance Table
    • Refine Abundance Table parameters
    • Refine Abundance Table output
  • Assign Taxonomies to Sequences in Abundance Table
  • Alpha Diversity
    • Alpha diversity measures
  • Beta Diversity
    • Beta diversity measures
  • PERMANOVA Analysis
  • Differential Abundance Analysis
  • Create Heat Map for Abundance Table
    • Clustering of features and samples
    • The heat map view
    • Create heat map for specific taxonomic level
  • Add Metadata to Abundance Table
• Find the best matching reference
  • Find Best Matches using K-mer Spectra
    • From samples best matches to a common reference for all
  • Find Best References using Read Mapping
    • The Find Best References using Read Mapping Report
• Phylogenetic trees using SNPs or k-mers
  • Create SNP Tree
    • SNP tree report
    • SNP tree
    • SNP Matrix
  • Create K-mer Tree
    • Visualization of K-mer Tree for identification of common reference
• MLST Scheme Tools
  • Getting started with the MLST Scheme tools
  • MLST Scheme Visualization and Management
  • Minimum Spanning Trees
    • The Minimum Spanning Tree view
    • Navigating the Tree view
    • The Layout panel
    • The Metadata panel
  • Type With MLST Scheme
    • Type With MLST Scheme results
    • The MLST Typing Result element
  • Add Typing Results to MLST Scheme
  • Identify MLST Scheme from Genomes
• Additional Typing Tools
  • Spoligotype Mycobacterium Tuberculosis
    • Spoligotype Mycobacterium Tuberculosis parameters
    • Spoligotype Mycobacterium Tuberculosis output
• Functional Analysis
  • Find Prokaryotic Genes
  • Annotate with BLAST
  • Annotate with DIAMOND
  • Annotate CDS with Best BLAST Hit
  • Annotate CDS with Best DIAMOND Hit
  • Annotate CDS with Pfam Domains
  • Build Functional Profile
    • Functional profile abundance table
  • Infer Functional Profile
  • Identify Pathways
    • Called Pathways Result
    • The Identified Pathways View
• Drug Resistance Analysis
  • Find Resistance with PointFinder
  • Find Resistance with Nucleotide Database
  • Find Resistance with ShortBRED
    • Resistance abundance table
  • Join Nearby Variants
• Databases for MLST Schemes
  • Create MLST Scheme
  • Download MLST Scheme
  • Import MLST Scheme
• Databases for Amplicon-Based Analysis
  • Download Amplicon-Based Reference Database
• Databases for Taxonomic Analysis
  • Download Curated Microbial Reference Database
    • Extracting a subset of a database
  • Download Custom Microbial Reference Database
    • Database Builder
  • Download Pathogen Reference Database
  • Create Taxonomic Profiling Index
• Databases for Functional Analysis
  • Download Protein Database
  • Download Ontology Database
    • The GO Database View
    • The EC Database View
  • Download Pathway Database
    • The Pathway Database
    • The Pathway View
  • Create DIAMOND Index
  • Import RNAcentral Database
  • Import PICRUSt2 Multiplication Table
• Databases for Drug Resistance Analysis
  • Download Resistance Database
  • Reference Data Elements
• QIAseq 16S/ITS Demultiplexer
• Utility Tools
  • Create Report from Table
  • Mask Low-Complexity Regions
    • Mask Low-Complexity Regions Report
  • Result Metadata
    • Create a Result Metadata Table
    • Running an analysis directly from a Result Metadata Table
    • Extend Result Metadata Table
    • Use Genome as Result
• Legacy tools
  • Extract Regions from Tracks
  • Analyze Viral Hybrid Capture Panel Data
• Appendix
  • Using the Assembly ID annotation
• Bibliography

Phylogenetic trees using SNPs or k-mers

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Subsections

• Create SNP Tree
• Create K-mer Tree

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