CHAMP Human Microbiome Profiler is now available in the CosmosID-HUBLearn More

CosmosID-HUB: Microbiome


1. Upload Your Raw Data

2. Choose Your Workflow

3. Upload Your Metadata

4. Create Comparative Analyses, Run Statistics & Interpret Your Data

CosmosID-HUB Microbiome

The CosmosID-HUB Microbiome is an online software solution that enables incredibly fast and easily accessible analysis of complex metagenomic data.

The app gives scientists user-friendly access to numerous pipelines developed by CosmosID, including amplicon and shotgun data analysis. In addition to having access to version-controlled, validated pipelines, the software enables continuous splicing of microbiome data for novel discoveries and appreciation of important analyses such as Principle Component Analysis, Alpha Diversity, Beta Diversity as well as significance testing between groups.

This means that you can begin analysing immediately interpreting your data as soon as sequencing is complete,  irrespective of how much computational infrastructure you have available to you!

The core benefits of the CosmosID pipeline includes but not limited to:

  • Characterize the functional potential of the microbiome community using MetaCyc Pathways, Enzyme Commission (EC), Pfam, CAZy and Go Terms.
  • Automated removal of host reads from raw sequencing reads for high microbial biomass specimens.
  • Validated and curated databases of microbial genomes to ensure everything in the database passes QC and that there are no chimeric assemblies, misclassifications or other errors!
  • Strain-level taxonomic classification with phylogenetic inference of novel organisms meaning you’re not relying on what has only been characterized in public databases. What does this mean? Should we identify a novel strain, we will simply call its nearest neighbour and teach you how to interpret the strain-level statistics we provide!
  • Multi-kingdom ID & characterization with one single pipeline: Bacteria, Viruses, Phages, Fungi, Protists, Bacterial MAG’s, AMR genes & Virulence Factors.
  • Precision Filters for confidence – CosmosID offers some of the most advanced machine learning filters for differentiating signal from noise, as demonstrated in various third-party challenges, meaning that the results are less impacted by false positives. 
  • Sample-type agnostic analysis. Whether you’re analysing stool, skin, cheese, wastewater or coral reefs, the CosmosID database is built agnostically to any specific sample type which gives you the flexibility to analyze multiple sample types across multiple projects over time and have the data continuity you need for long-term and continuous R&D!

Power your research. Find out more about our award-winning Microbiome analysis.

bioinformatics analysis as part of our services

CosmosID-HUB MicrobiomeWhat are the advantages of the CosmosID-HUB Microbiome?

Usability & Access
Analysis & Data Usage

CosmosID-HUB MicrobiomeIs the CosmosID-HUB Microbiome right for me?

The CosmosID-HUB Microbiome has been built to be flexible and to enable access for scientists with varying degrees of bioinformatics experience in mind. Between the user-friendly interface and the Command Line Interface (CLI), the pipeline can be used in isolation or integrated with your existing workflows. So whether you just want the profiling results or complete visualizations ready for export, the CosmosID-HUB Microbiome can complement what you’re already doing or what you’d like to do moving forward!

CosmosID-HUB MicrobiomeHow do I access the CosmosID-HUB Microbiome and what data can I upload?

Simply visit The CosmosID App to access the CosmosID-HUB Microbiome, where you can create a free account. No subscription is needed – just purchase credits and start your analysis. There are example datasets so you can get a feel for the functionality!

Depending on your needs:

Further documentation on the CosmosID-HUB Microbiome can be found in our quick startup guide, including the upload process.

Book a demo with a member of the business development team here:


Get in Touch To Request Free Demo and Trial

CosmosID-HUB MicrobiomeFrequently Asked Questions

How many users can access data once sequenced or uploaded?

Once sequenced data is uploaded into your account, we can then transfer this to as many colleagues or collaborators as is requested.

Can you export the visualisations and tables from the CosmosID-HUB Microbiome?

Yes – all visualisations, charts and tables can be easily exported in a variety of file formats.

Are there limits to the upload file size?

There are provisional limits of 30GB (7.5GB .gz) for shotgun and 1GB (250MB .gz) for amplicon sequencing; however if your file of interest exceeds this, please reach out to and we can create a custom upload link.