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QIAGEN CLC Microbial Genomics Module

Advanced tools and databases for microbial genomics – without the guesswork

QIAGEN CLC Microbial Genomics Module is a plugin extension to QIAGEN CLC Genomics Workbench. It is included in our QIAGEN CLC Genomics Premium offering, and is compatible with our enterprise solutions (QIAGEN CLC Genomics Cloud Engine and QIAGEN CLC Genomics Server).

QIAGEN CLC Microbial Genomics Module provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

Antimicrobial resistance characterizations

The QIAGEN CLC Microbial Genomics Module provides extensive tools to support advanced bioinformatics and genomics analysis of antimicrobial resistance (AMR) genes and markers. The tools specifically developed for AMR include those for analysis of both assembled isolate genomes or metagenomes, as well as tools for the assembly-free detection of AMR markers directly from your FASTQ data.
Extensive integrated access to multiple AMR databases include Comprehensive Antimicrobial Resistance Database (CARD) (1), ResFinder (2), ARG-ANNOT (3), NCBI Bacterial Antimicrobial Resistance Reference Gene Database (4), PointFinder (5) and VFDB (6) databases. In addition, as part of QIAGEN’s commitment to the US Center for Disease Control’s Global AMR Challenge, we provide an additional novel resource for AMR research: The QIAGEN Microbial Insights AR (QMI-AR) database.

Advanced tools for bacterial strain typing

Whether you’re focused in the areas of public health epidemiology, clinical microbiology research or basic microbial genomics research, QIAGEN CLC Microbial Genomics Module provides you with state of the art tools for strain typing bacterial, fungal and viral genomes. For bacterial isolates, users benefit from tools for traditional MLST-, cgMLST-, wgMLST- or SNP-based analysis and advanced assembly-free k-mer-based strain typing. The tools also provide direct access to pubMLST.org and other online public databases with internationally recognized schemas. Collectively, these tools provide researchers with total flexibility in one tool set for the analysis of isolates – regardless whether it’s a virus, bacteria or fungal genome.

The QIAGEN CLC Microbial Genomics Module also includes an interactive ‘Minimum Spanning Tree’ (MST) visualization for instant and intuitive overview for outbreak analysis.

Microbiome profiling and functional metagenomics

QIAGEN CLC Microbial Genomics Module offers unparalleled options for analysis of both amplicon/OTU and whole metagenome sequencing data. The tools provide a fully integrated solution for everything from 16S/ITS microbiome profiling, shotgun metagenomics profiling, metagenomics assembly, automated gene finding and annotation with BLAST or DIAMOND. The software also provides innovative tools for binning of contigs from de novo assemblies – an important step in identifying plasmids and other mobile elements. All of these tools can also connect to a variety of established public databases, available for direct download within QIAGEN CLC, or use databases built and curated by the users themselves.

System requirements

For the general requirements, please refer to the relevant
QIAGEN CLC Workbench system requirements.

For the specific system requirements for QIGEN CLC Microbial Genomics Module, please see here.

Latest improvements

We frequently release updates and improvements such as new functionalities, bug fixes or plugins. A full list of recent changes is included on the latest improvements page.

Key features
  • Antimicrobial resistance detection and gene finding
  • Identifies resistances, acquired genes and mutations, both in metagenomic or isolate NGS samples
  • Access to leading Antimicrobial Resistance Gene Databases QMI-AR, CARD, ResFinder and PointFinder
  • Access to Marker Databases derived from the QMI-AR, CARD and ARG-ANNOT resources
  • Find genes on finished genomes or contigs and annotate with PFAM, Gene Ontology and BLAST or DIAMOND
  • Microbiome profiling
  • Taxonomic profiling of amplicon and full metagenomic data
Key features (continued)
  • De novo or reference based OTU-clustering of 16S, 18S and ITS amplicon data
  • Easy access to common reference databases such as Greengenes, Silva and UNITE
  • Custom-built genome reference database by direct import of microbial genomes from NCBI provides the highest precision of taxonomic assignment
  • Metagenome de novo assembly, binning of contigs, gene finding and functional profiling of microbiomes using PFAM, Gene Ontology and BLAST
  • Stacked bar charts, area charts, sunburst charts and heat maps to explore and compare the taxonomic composition of samples or sample groups
  • User-friendly statistical tools deliver class-leading performance for Alpha and Beta diversity estimation, PERMANOVA Analysis and Differential Abundance Analysis
  • Pathogen Typing and Outbreak Analysis
  • Automated identification and characterization of microbes using whole genome data; a single easy-to-use workflow reports NGS-MLST, taxonomy, closest known reference genome and antimicrobial resistance genes for microbial isolates
  • K-mer trees and whole genome SNP trees for accurate outbreak investigation and source tracking of pathogens


1. Jia, B. et al. (2017) CARD 2017: Expansion and Model-Centric Curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research 45: D566–73.
2. Zankari, E. et al. (2012) Identification of Acquired Antimicrobial Resistance Genes. The Journal of Antimicrobial Chemotherapy 67: 2640–2644.
3. Gupta, S. et al. (2014). ARG-ANNOT, a New Bioinformatic Tool to Discover Antibiotic Resistance Genes in Bacterial Genomes. Antimicrobial Agents and Chemotherapy 58: 212–220.
4. Feldgarden, M et al. (2019) Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrobial Agents and Chemotherapy A63: e00483-19.
5. Zankari, E. et al. (2017) PointFinder: A Novel Web Tool for WGS-Based Detection of Antimicrobial Resistance Associated with Chromosomal Point Mutations in Bacterial Pathogens. The Journal of Antimicrobial Chemotherapy 72: 2764–2768.
6. Liu, B. et al. (2019) VFDB 2019: A Comparative Pathogenomic Platform with an Interactive Web Interface. Nucleic Acids Research 47: D687–D692.