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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 Small Genome
De Novo Assemble Small Genome parameters
De Novo Assemble Small Genomes output
De Novo Assemble Metagenome
De Novo Assemble Metagenome parameters
De Novo Assemble Metagenome output
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
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
Identify Viral Integration Sites
The Viral Integration Viewer
The Viral Integration Report
Classify Whole Metagenome Data
Classify Whole Metagenome Data parameters
Classify Whole Metagenome Data output
Classify Whole Metagenome Data abundance table
Taxonomic Profiling
Taxonomic Profiling parameters
Taxonomic Profiling output
Taxonomic Profiling abundance table
Abundance Analysis
Merge Abundance Tables
Merge Abundance Tables output
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
Download Custom Microbial Reference Database
Database Builder
Download Pathogen Reference Database
Create Whole Metagenome Index
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
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
Remove OTUs with Low Abundance
Appendix
Using the Assembly ID annotation
Bibliography
Databases for Functional Analysis
Subsections
Download Protein Database
Download Ontology Database
Download Pathway Database
Create DIAMOND Index
Import RNAcentral Database
Import PICRUSt2 Multiplication Table