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QIAGEN CLC Microbial Genomics Module

Analysis of microbial genomics and metagenomics made easy!

The QIAGEN CLC Microbial Genomics Module offers tools and workflows for a broad range of bioinformatics needs for microbiome analysis, isolate characterization, functional metagenomics and resistance identification. The module extends the capabilities of QIAGEN CLC Genomics Workbench to support analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes. It is also compatible with both the QIAGEN CLC Genomics Cloud Engine and QIAGEN CLC Genomics Server.

Microbiome taxonomic profiling

QIAGEN CLC Microbial Genomics Module offers unparalleled options for analysis of both amplicon/OTU and whole metagenome sequencing data. NGS data is easily analyzed using OTU clustering or taxonomic profiling tools and can then be aggregated for large-scale comparative genomics studies using CLC’s metadata tools. Start metagenome analysis on day one with two preconfigured workflows for data QC, removal of contaminating data originating from host DNA, OTU Clustering or Taxonomic Profiling tools, and estimation of alpha and beta diversity. Easy-to-use statistical tools enable comparison of microbial communities across many samples.

Advanced tools for typing of microbial genomes

Whether you’re focused on public health epidemiology, clinical microbiology research or basic microbial genomics research, QIAGEN CLC Microbial Genomics Module provides state-of-the-art tools for strain typing of bacterial, fungal and viral genomes. For bacterial isolates, users benefit from the Identify MLST tool, which enables rapid typing and comparative genomics using globally accepted schemas from multiple public MLST databases, along with tools to download and modify those schemas based on each lab’s specific needs. QIAGEN CLC Microbial Genomics Module also provides assembly- and reference-free tools including the Find Best Matches using K-mer Spectra and Create K-mer Tree tools, which are especially useful for organisms for which MLST typing is not appropriate, such as viruses or fungi. In addition, users have the option of using our Create SNP Tree tool to compare novel isolates to gold-standard reference genomes using a read-mapping and SNP variant calling approach. 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.

Antimicrobial resistance characterization

To support you in the fight against the worldwide threat of emerging antimicrobial resistant (AMR) pathogens, a comprehensive set of tools and databases designed to work together are readily available for download and immediate use. 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.

These tools are further enhanced by integrated access to popular, publicly available databases for AMR and virulence factor characterization, including the Comprehensive Antimicrobial Resistance Database (CARD) (1), ResFinder (2), ARG-ANNOT (3), NCBI Bacterial Antimicrobial Resistance Reference Gene Database (4), PointFinder (5) and VirDB (6) databases. Furthermore, as part of QIAGEN’s commitment to develop novel resources and tools for AMR research, the QIAGEN CLC Microbial Genomics Module includes two unique databases for AMR bioinformatics research: QIAGEN Microbial Insights AR (QMI-AR) database and ARES-Genetics ARESdb.

De novo assembly of isolates and metagenomes

If you are interested in understanding the underlying functional classes of genes and organisms in your sample, then QIAGEN CLC Microbial Genomics Module can help you. Users can carry out assembly of both individual genomes or metagenomes with QIAGEN CLC’s best-in-class de novo assembler. Our core assembly tool, De Novo Assemble, can be used for a huge range of genomes from all branches of the of the phylogenetic tree. For example, it could be used for assembling novel RNA viruses for the FDA ARGOS Genome Standards Project (7), or for succeeding where other assemblers failed in assembling the largest eukaryotic genome ever attempted (8). In addition, within QIAGEN CLC Microbial Genomics Module, we include an optimized assembler for metagenomics samples, De Novo Assemble Metagenome, that has been shown to perform exceptionally well with large and complex metagenomics samples. For an example of a large-scale metagenomics assembly using QIAGEN CLC’s de novo assembler, see the Parks et. al. 2017 study in Nature Microbiology (9)where they recovered over 8000 novel genomes from SRA.

Functional metagenomics – Go beyond the assembly

Following de novo assembly, there are numerous additional tools within QIAGEN CLC Microbial Genomics Module to assist researchers in deeply characterizing their samples without the need to use command line tools. This includes tools for binning contigs into distinct groups using our Bin Pangenomes by Sequence or Bin Pangenomes by Taxonomy tools, which can be used to identify plasmids and “metagenomic assembled genomes” (MAGs) from within metagenomics data. For assemblies of bacterial microbiome samples, users can leverage the Find Prokaryotic Genes tools to identify coding sequences (CDSs). These CDSs can then be annotated with the Annotate CDS with BLAST or DIAMOND tools, and characterized using Gene Ontology classifications or by identifying PFAM domains contained within them. Collectively, these tools can be used for functional metagenomics or metatranscriptomic analysis of microbiome samples.

Quick and easy reference database customization

Using the right reference data is crucial for accurate microbial genomics research, whether you’re working with complex microbiome samples or isolates of specific strains. While it’s possible to download over 200,000 genomes from NCBI directly within QIAGEN CLC Microbial Genomics Module, the larger your database, the greater the need to curate and maintain the contents of it. Database size and content also affect compute resource requirements and specificity of your downstream tools. The new Create Microbial Reference Database tool is designed to overcome these common challenges in metagenome analysis. For exploration of microbial diversity in novel sample types, use a comprehensive database. For highest precision and faster turnaround time in routine use, simply remove irrelevant taxa from the reference database. In addition, you can download specific references from the NCBI Pathogen Project.

 

 Supported features

  • Antimicrobial resistance detection and gene finding
  • Identifying resistances, acquired genes and mutations, 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
  • 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 for highly precise 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 leading-class 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

Read the latest improvements here.

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References

  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.
  7. Sichtig, H. et al. (2019) FDA-ARGOS Is a Database with Public Quality-Controlled Reference Genomes for Diagnostic Use and Regulatory Science. Nature Communications 10 (1): 3313.
  8. Kuzmin, D. et al. (2019) Stepwise Large Genome Assembly Approach: A Case of Siberian Larch (Larix Sibirica Ledeb). BMC Bioinformatics 20 (S1): 37–52.
  9. Parks, D. et al. (2017) Recovery of Nearly 8,000 Metagenome-Assembled Genomes Substantially Expands the Tree of Life. Nature Microbiology 2 (11): 1533–1542.

 

 

Downloads

Plugin Manual
Online manual Download manual
Plugin Download
Download plugin
Download CLC Microbial Genomics Module

Version

Platform support

Download

20.0.0

QIAGEN CLC Genomics Workbench


 [20.0.1, 20.0]

4.8.0

QIAGEN CLC Genomics Workbench


 [12.0.3]

4.5.0

QIAGEN CLC Genomics Workbench


 [12.0.2, 12.0.1]

4.1.0

QIAGEN CLC Genomics Workbench


 [12.0]

3.6.1

Biomedical Genomics Workbench


 [5.0.2, 5.0.1]

QIAGEN CLC Genomics Workbench


 [11.0.2, 11.0.1]

3.0.0

Biomedical Genomics Workbench


 [5.0.0]

QIAGEN CLC Genomics Workbench


 [11.0.0]

2.5.5

Biomedical Genomics Workbench


 [4.1.3, 4.1.2]

QIAGEN CLC Genomics Workbench


 [10.1.3, 10.1.2]

2.5.1

Biomedical Genomics Workbench


 [4.1.1, 4.1.0]

QIAGEN CLC Genomics Workbench


 [10.1.1, 10.1.0]

2.0.0

Biomedical Genomics Workbench


 [4.0]

QIAGEN CLC Genomics Workbench


 [10.0.1, 10.0]

1.6.2

Biomedical Genomics Workbench


 [3.5.4]

QIAGEN CLC Genomics Workbench


 [9.5.4]

1.6.1

Biomedical Genomics Workbench


 [3.5.3, 3.5.2, 3.5.1, 3.5]

QIAGEN CLC Genomics Workbench


 [9.5.3]

1.5.1

Biomedical Genomics Workbench


 [3.0.1, 3.0]

1.4.1

Biomedical Genomics Workbench


 [2.5.4, 2.5.3]

QIAGEN CLC Genomics Workbench


 [8.5.4]

1.2.2

Biomedical Genomics Workbench


 [2.5.2]

1.2.1

Biomedical Genomics Workbench


 [2.5.1, 2.5]

1.0

Biomedical Genomics Workbench


 [2.1.2, 2.1.1, 2.1]
Server plugin Downloads
Download plugin
Download CLC Microbial Genomics Server Extension

Version

Platform support

Download

20.0.0

QIAGEN CLC Genomics Server


 [20.0.1, 20.0]

4.8.0

QIAGEN CLC Genomics Server


 [11.0.3]

4.5.0

QIAGEN CLC Genomics Server


 [11.0.2, 11.0.1]

4.1.0

QIAGEN CLC Genomics Server


 [11.0]

3.6.1

Biomedical Genomics Server Solution


 [10.0.2, 10.0.1]

QIAGEN CLC Genomics Server


 [10.0.2, 10.0.1]

3.0.0

Biomedical Genomics Server Solution


 [10.0]

QIAGEN CLC Genomics Server


 [10.0.0]

2.5.5

Biomedical Genomics Server Solution


 [9.1.3, 9.1.2]

QIAGEN CLC Genomics Server


 [9.1.3, 9.1.2]

2.5.1

Biomedical Genomics Server Solution


 [9.1.1, 9.1]

QIAGEN CLC Genomics Server


 [9.1.1, 9.1.0]

2.0.0

Biomedical Genomics Server Solution


 [9.0]

QIAGEN CLC Genomics Server


 [9.0]

1.6.2

Biomedical Genomics Server Solution


 [8.5.4]

QIAGEN CLC Genomics Server


 [8.5.4]

1.6.1

Biomedical Genomics Server Solution


 [8.5.3, 8.5.2, 8.5.1, 8.5]

QIAGEN CLC Genomics Server


 [8.5.3]

1.5.1

Biomedical Genomics Server Solution


 [8.0.1, 8.0]

1.4.1

Biomedical Genomics Server Solution


 [7.5.4, 7.5.3]

1.2.2

Biomedical Genomics Server Solution


 [7.5.2]

1.2.1

Biomedical Genomics Server Solution


 [7.5.1, 7.5]

1.0

Biomedical Genomics Server Solution


 [7.0.3, 7.0.2, 7.0.1, 7.0]
Application Notes and Tutorials
Application Notes and Tutorials
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Webinars
Product Page
Product Page
Latest Improvements
Latest Improvements

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