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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

Download Curated Microbial Reference Database

The Download Curated Microbial Reference Database tool downloads selected references as sequence lists and/or indexes that can be used with downstream analysis tools.

To run the tool, go to:

        Tools | Microbial Genomics Module () | Metagenomics () | Databases () | Taxonomic Analyses () | Download Curated Microbial Reference Database ()

In the first window (figure 16.1), select the database you wish to download.

Figure 16.1: Select the database and output format

You can choose between several databases:

• QMM-H. QIAGEN Microbial Metagenome - Human Host database is a comprehensive microbial reference database for classification of whole metagenome data with Classify Whole Metagenome Data (Classify Whole Metagenome Data). The database contains RefSeq genomes of archaea, bacteria, viruses, protozoa and fungi, and UniVec_Core sequences. Genome sequences and annotations are from Genbank (https://www.ncbi.nlm.nih.gov/genbank/). UniVec_Core sequences are from the UniVec Database (http://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/).
  Size of sequence list/index: 90.3 GB/89.5 GB.

• QMI-PTDB Genus. QIAGEN Microbial Insights - Prokaryotic Taxonomy Database is a microbial reference database for taxonomic profiling of bacteria and archaea. The database represents all genera with a varying number of species per genus.
  Genome sequences and annotations are from the NCBI Reference Sequence Database (RefSeq; https://www.ncbi.nlm.nih.gov/refseq/) and have been annotated with taxonomy from the Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org).
  The database was created by selecting one representative genome per species, and subsequently reducing the relative number of species per genus to meet the desired database size. For reduction, higher assembly status, lower number of contigs, and longer total length was prioritized. All genomes marked as "reference genome" were retained. So were species commonly included in microbial reference standards.
  When running Taxonomic Profiling with the QMI-PTDB Genus database, 32GB of memory is required.
  Size of sequence list/index: 15.7 GB/22.4 GB.

• QMI-PTDB Family. QIAGEN Microbial Insights - Prokaryotic Taxonomy Database is a microbial reference database for taxonomic profiling of bacteria and archaea. The database represents all families with a varying number of genera per family.
  Genome sequences and annotations are from the NCBI Reference Sequence Database (RefSeq; https://www.ncbi.nlm.nih.gov/refseq/) and have been annotated with taxonomy from the Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org).
  The database was created by selecting one representative genome per genus, and subsequently reducing the relative number of genera per family to meet the desired database size. For reduction, higher assembly status, lower number of contigs, and longer total length was prioritized. All genomes marked as "reference genome" were retained. So were species commonly included in microbial reference standards.
  When running Taxonomic Profiling with the QMI-PTDB Family database, 16GB of memory is recommended.
  Size of sequence list/index: 4.6 GB/6.5 GB.

• Unified Human Gastrointestinal Genome (UHGG). A database of metagenomic-assembled genomes from human gut samples, curated and hosted by MGnify [Gurbich et al., 2023], EMBL-EBI (https://www.ebi.ac.uk/metagenomics/browse/genomes).
  Size of sequence list/index: 3.5 GB/7.8 GB.

• Chicken Gut. A database of metagenomic-assembled genomes from chicken gut samples, curated and hosted by MGnify [Gurbich et al., 2023], EMBL-EBI (https://www.ebi.ac.uk/metagenomics/browse/genomes).
  Size of sequence list/index: 1.0 GB/2.1 GB.

• Pig Gut. A database of metagenomic-assembled genomes from pig gut samples, curated and hosted by MGnify [Gurbich et al., 2023], EMBL-EBI (https://www.ebi.ac.uk/metagenomics/browse/genomes).
  Size of sequence list/index: 1.0 GB/2.0 GB.

• Unclustered Reference Viral DataBase (U-RVDB). Unclustered Reference Viral Database for virus detection [Goodacre et al., 2018]. The database includes curated viral, virus-related and virus-like nucleotide sequences except bacterial viruses, which are excluded.
  Size of sequence list/index: 1.0 GB/5.1 GB.

• Clustered Reference Viral DataBase (C-RVDB). Clustered Reference Viral Database for virus detection [Goodacre et al., 2018]. The database includes curated viral, virus-related and virus-like nucleotide sequences except bacterial viruses, clustered at 98% sequence similarity.
  Size of sequence list/index: 0.4 GB/1.9 GB.

• ViraCura^TM HPV REF. A curated database of Human Papillomavirus reference strains. It contains unmodified viral reference genomes and associated record information from NCBI databases.
  Size of sequence list/index: 1.1 MB/1.2 MB.

• ViraCura^TM HPV VAR. A curated database of Human Papillomavirus variants of reference strains. It contains unmodified viral reference genomes and associated record information from NCBI databases.
  Size of sequence list/index: 0.3 MB/0.8 MB.

• ViraCura^TM ANIMAL PV. A curated database of Animal Papillomavirus. It contains unmodified viral reference genomes and associated record information from NCBI databases.
  Size of sequence list/index: 1.1 MB/1.2 MB.

• MPXV. A curated database of Monkeypox virus reference strains. It contains unmodified viral reference genomes and associated record information from NCBI databases, as well as metadata and customized taxonomic nomenclature.
  Size of sequence list/index: 17.2 MB/36 MB.

• MOCOVA. A curated database of Monkeypox outgroup reference strains (Molluscum contagiosum, Cowpox, Variola, and Vaccinia). It contains unmodified viral reference genomes and associated record information from NCBI databases, as well as metadata and customized taxonomic nomenclature.
  Size of sequence list/index: 0.4 MB/0.6 MB.

When you have made your database selection, choose which format you wish to download.

• Download Database as Sequence list. Produces an annotated sequence list.

Depending on the database selection, one of the following will be available:

• Download Database as Whole Metagenome Index. This index type is used by the Classify Whole Metagenome Data tool (Classify Whole Metagenome Data).
• Download Database as Taxonomic Profiling Index. This index type is used by e.g., the Taxonomic Profiling tool (Taxonomic Profiling).

Some of the databases offered are derived work, licensed under a Creative Commons Attribution-ShareAlike (CC BY-SA) license. We offer free access to those without requiring a CLC product license. They can be downloaded using the CLC Genomics Workbench with the Microbial Genomics Module installed in Viewing Mode. The downloaded files can then be exported to non-proprietary formats.

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