CosmosID Plugin for CLC

Microbiome analysis with strain level accuracy

Ease-of-use meets industry-leading accuracy in the new CosmosID plugin for CLC Genomics and Biomedical Genomics Workbench. Detect pathogens and antimicrobial resistance genes, or track microbial community changes.


Identify microbes and antimicrobial resistance factors

CosmosID identifies bacteria, viruses, fungi, parasites and antibiotic resistance factors in shotgun metagenomic data and is able to discriminate pathogens from their ‘near neighbors’ using statistical and computational methods, with no prior assumptions as to what is present in the sample.

Analyze 12 of your own samples, free of charge.

Request free samples. Available to new users only.


Deeper insight through expert curated reference data

CosmosID uses raw, unassembled reads as input and matches the sequence against GenBook®, a curated reference database of known pathogens and microbes including bacteria, viruses, fungi, parasites, and antibiotic resistance and virulence factors. GenBook® is derived from private and public databases of assembled genomes, and constitutes hundreds of millions of marker sequences representing both coding and non-coding sequences that are shared or uniquely identified across taxonomic or phylogenetic levels.

Try it out

Watch our video tutorial and start exploring the CosmosID plugin. Trial users can use the following credentials for setting up a demo-account.

User name: [email protected]
Password: cid123


Accelerate your metagenomics project

  • Superior performance compared to open source tools
  • Ultrafast bioinformatics (results in minutes)
  • Ease of Use through direct access to powerful statistics, interactive visualizations and a plethora of NGS tools built for microbiology through seamless integration into CLC Workbenches and QIAGEN Microbial Genomics Pro Suite.
  • Query the largest curated database in the industry comprising bacteria, viruses, fungi, parasites, antibiotic resistance genes, and virulence markers
  • Phylogenetic placement for identification
  • Characterization of community resistome and virulome
  • Precise identification at sub-species and/or strain level



The plugin is fully compatible with the Microbial Genomics Pro SuiteCLC Genomics Workbench*, and Biomedical Genomics Workbench*

* The plugin requires an up to date version of the CLC Microbial Genomics Module to be installed.








Plugin Manual

Download manual

Plugin Download

Download plugin

Download CosmosID


Platform support



Biomedical Genomics Workbench

 [5.0.1, 5.0.0]

CLC Genomics Workbench

 [11.0.1, 11.0.0]


Biomedical Genomics Workbench

 [4.1.2, 4.1.1, 4.1.0, 4.0]

CLC Genomics Workbench

 [10.1.2, 10.1.1, 10.1.0, 10.0.1, 10.0]


Biomedical Genomics Workbench

 [3.5.4, 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1, 3.0]

CLC Genomics Workbench

 [9.5.4, 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1, 9.0]

Step 1 - About you

Step 2 - Organizational details

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