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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 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
    • 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
  • 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
• Introduction to Typing and Epidemiology
• 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
• 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
• 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
    • ARES Database
• 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
  • Extract Regions from Tracks
  • Analyze Viral Hybrid Capture Panel Data
• Appendix
  • Using the Assembly ID annotation
• Bibliography

Database Builder

Depending on your internet connection, it takes a few seconds to download the content and open the Database Builder (figure 15.5).

Figure 15.5: Search, filter and select assemblies to download.

Assemblies that match the criteria from the Download Custom Microbial Reference Database tool will be pre-selected, indicated by a "Yes" in the Included column.

The Database Builder table contains additional columns with metadata based on information from GenBank, https://www.ncbi.nlm.nih.gov/genbank/. Use the Database Builder functionality described below to customize and define the reference set to be downloaded.

Use the filtering options located at the top right to filter the table. For information on how to use the simple and advanced table filters, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Filtering_tables.html.

From the Side Panel on the right, the following option is available:

• Aggregate rows on taxonomy. Aggregates results by the selected taxonomic level, e.g. Order.

Below the table you find buttons for quick selection, including or excluding rows, and download of selected reference subset:

• Quick selection. For selection of one of the following predefined subsets, based on information in the Assembly Status, Chromosomal scaffolds, and In RefSeq columns:
  • Single scaffold complete genomes in RefSeq. Complete genomes with Chromosomal scaffolds= 1; In RefSeq= Yes.
  • Complete genomes in RefSeq. Complete genomes with In RefSeq= Yes.
  • All complete genomes. Any Complete genome.
  "Complete genome" refers to the Assembly Status. All genomes marked as Complete genome or Chromosome are included in the subsets, as are any reference marked as representative genome (repr) or reference genomes (refr).
• Include and Exclude. Includes or excludes the selected rows from the subset selection.
• Reset selection. Reset selection to match criteria specified in Download Custom Microbial Reference Database wizard.
• Download selection. For download of the selected reference subset. Brings up a dialog with the following options (figure 15.6):
  • Include all annotation tracks. Will include CDS, gene, etc. annotations in the downloaded database. The annotations are not needed for taxonomic profiling, but may be required for other applications such as creating MLST schemes.
  • Minimum contig length. The minimum length of sequences to be included in the database.

    The dialog provides an estimate of the memory and disk requirements needed to later run the Taxonomic Profiling tool with the database you are about to download.

  
  Figure 15.6: Filter options for download of the selected references.

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