Microbiome Profiling

Streamline Microbiome Profiling with Cosmos-Hub

Cosmos-Hub allows researchers to import their raw sequencing data directly into the platform and run a number of available bioinformatics pipelines for microbiome analysis.

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Microbiome Profiling

Unlock expert microbial community profiling for all types of microbiome research—human, non-human, and environmental. Cosmos-Hub delivers reliable, publication-ready results using cloud-powered, no-code pipelines for both large-scale and focused projects, enabling robust microbiome analysis of microbial communities and microbial diversity across the human microbiome and wider environments.

Import raw sequencing data (e.g., amplicon 16S/ITS/18S rRNA data, shotgun metagenomics) directly into the platform to run industry-leading bioinformatics workflows for robust taxonomic and functional analysis. Whether you’re studying the oral microbiome, gut microbiome, vaginal microbiome, skin microbiome, animal microbiomes, or microbiota from soil, water, and other ecosystems, Cosmos-Hub supports complex microbial community analysis with speed and precision.
 

Our Microbiome Profiling Analysis Software Process

 
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Microbiome Profiling

Streamline Microbiome Profiling with Cosmos-Hub

Cosmos-Hub allows researchers to import their raw sequencing data directly into the platform and run a number of available bioinformatics pipelines for microbiome analysis.
Microbiome Profiling
 

In just a few easy steps, users can run industry-leading bioinformatics pipelines for a wide range of different data types:

  • Import data from their computer, from Illumina BaseSpace, directly from NCBI SRA or via Command Line Import (CLI).
  • Select the type of data they’d like to import: Shotgun, 16S or ITS
  • Select from 1 of 9 different host genomes to run automated host read depletion
  • Upload your study metadata
  • Choose your pipeline and primers
 

In just a few easy steps, users can run industry-leading bioinformatics pipelines for a wide range of different data types:

  • Import data from their computer, from Illumina BaseSpace, directly from NCBI SRA or via Command Line Import (CLI).
  • Select the type of data they’d like to import: Shotgun, 16S or ITS
  • Select from 1 of 9 different host genomes to run automated host read depletion
  • Upload your study metadata
  • Choose your pipeline and primers
Microbiome Profiling
Cosmos-Hub agnostically supports data generated by all sequencing technologies
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Why Run Your Samples in Cosmos-Hub?

 

You’ve put significant effort into collecting your microbiome samples—be it saliva, stool, skin swabs, environmental swabs, wastewater, or other sample types. Once nucleic acids are extracted, libraries prepared, and DNA sequencing complete, accurate profiling becomes the critical step in translating raw reads and genetic material into meaningful biological insights about microbiome composition.

Your choice of computational methods and bioinformatics pipelines directly shapes how microbial communities are classified, compared, and functionally annotated. Cosmos-Hub ensures reproducible, high-quality results that enable discoveries across clinical, research, and environmental domains.

 

Microbiome Profiling Software Key Features

The Cosmos-Hub team have built and curated microbial genomics pipelines optimised for various sequencing technologies, so you can make the most of your data and minimise the effect from sequencing errors!​

 
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Standardized & Reproducible

All pipelines are version-controlled to ensure standardization across your studies and between your team, supporting robust statistical analysis of species abundance data, alpha diversity, and beta diversity in line with leading microbiome research.

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No-Code Platform

Run any pipeline without coding skills. All pipelines have been made available to run in a series of simple steps.

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FastQC/MultiQC

In addition to running your pipeline of choice, make sure your sequencing run was successful by running FastQC on your samples.

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Convenience

Don’t fill up your local storage by simply importing directly from Illumina BaseSpace or NCBI SRA.

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No Specialized Infrastructure Required

Save costs on servers and specialized computers by leveraging Cosmos-Hub’s cloud infrastructure. All you need is an internet connection and Google Chrome. That’s it!

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Speed to results

Cosmos-Hub pipelines perform up to 19X faster than alternatives, allowing you to go from raw data to profiles in a matter of a few hours.

Why Choose Cosmos-Hub for Microbiome Profiling?
 
Cosmos-Hub is a comprehensive solution for microbiome research of all types—from oral and gut microbiome studies to environmental and comparative ecology projects. Supporting both shotgun metagenomics and amplicon sequencing, the platform enables accurate profiling of bacteria, archaea, fungi, protists, and viruses across diverse ecosystems.
 
 
Feature Profiling Function
Industry-Leading Pipelines Access CHAMP™, Kepler™, EMU, DADA2, and Functional 2.0 for state-of-the-art taxonomic and functional profiling.
Wide Data Compatibility Supports analysis of shotgun and amplicon sequencing data targeting the 16S rRNA gene, ITS and 18S for fungal community profiling, using both short and long-read sequencing—enabling profiling across microbial taxa including bacteria, fungi, archaea, viruses, and protists within human and non-human microbiomes and environmental samples.
Accurate & Fast Results In-house developed algorithmic advances and curated reference databases deliver high recall, low false positives, and rapid analysis of microbiome composition, beta diversity, and microbial abundances, critical for microbiota studies.
Comprehensive Functional Insights Annotates microbial pathways and metabolic pathways (e.g., Gut-Brain, Gut-Metabolic Modules, KEGG, MetaCyc, GO Terms and many more), linking identified microbial taxa to specific gene families and biological functions within the microbiome
AMR & Virulence Detection Enables direct detection of antibiotic resistance genes and virulence factors from raw sequencing reads, using marker gene and genome-resolved approaches—vital for understanding microbiome interactions and potential human health risks as well as spread of resistance throughout the environment.
Targeted & Untargeted Profiling Combines community profiling tools (DADA2 for 16S amplicon data, QIIME for ITS profiling, Emu for long-read and whole-community shotgun sequencing) to capture both targeted sub-communities and the full spectrum of microbial species, including rare bacterial species and strains in rare and exotic sample types.
Standardized & Reproducible Version-controlled workflows allow users to re-run, review, and compare statistical analyses and further analysis across dataset versions, ensuring robust scientific and clinical research outcomes.
Flexible & Scalable Cloud-based infrastructure processes anything from small microbiome projects to large-scale studies (thousands of samples) with quick turnaround.
User-Friendly & No-Code Accessible web interface for microbiome data analysis; requires no bioinformatics expertise or coding, making it usable by clinicians and researchers alike.

 

The Cosmos-Hub Pipelines

Best-in-Class Taxonomic and Functional Profiling for Human Microbiome Studies

CHAMP™ is a state-of-the-art, published pipeline built on over 400,000 metagenome-assembled genomes (MAGs) from more than 30,000 human microbiome samples across nine body sites.

It delivers unmatched species-level resolution of bacteria, archaea, eukaryotes, and phages with 16% higher recall and 400x lower false positive rate than other leading tools.

Moreover, CHAMP™ integrates functional annotation via Gut-Brain Modules (GBMs), Gut-Metabolic Modules (GMMs), and KEGG pathways. This pipeline has empowered published research on microbiome-linked health outcomes, probiotics, and population-scale microbiome studies.

To learn more, download the whitepaper here: http://www.cosmos-hub.com/content-library

Comprehensive metagenomics for planetary microbiomes beyond humans

Kepler™ combines exact k-mer matching with probabilistic alignment to generate microbiome profiles for bacteria, fungi, viruses & protists from shotgun data.

Kepler™ allows researchers to understand the nearest neighboring reference genome in the database at sub-species level. Its meticulously curated database, GenBook™, and patented algorithm efficiently identify taxa, even in low-biomass or host-contaminated samples. 

Benchmarking studies highlight Kepler™’s superior sensitivity, accuracy, and speed compared to Kraken, MetaPhlAn4, and other standard tools, making it ideal for microbiome discovery across clinical, agricultural, and environmental domains.

Comprehensive Microbiome Function Mapping via Multi-Database Annotation

Cosmos-Hub offers Kepler™ in combination with a host-agnostic functional pipeline, Functional 2.0, which interrogates shotgun metagenomic and metatranscriptomic data to understand metabolic and biochemical potential by annotating translated reads with numerous functional databases:

  • MetaCyc Pathways,
  • Enzyme Commissions,
  • Pfam,
  • CAZy,
  • GO Terms.

Abundance normalization (copies per million) ensures comparability across samples with variable depth. With intuitive visualizations and extensive feature descriptions, Functional 2.0 enables users to explore microbial gene function, pathway information, and environmental or health associations with clarity.

To learn more, download the whitepaper here: http://www.cosmos-hub.com/content-library

 

Comprehensive Microbiome Function Mapping via Multi-Database Annotation

Cosmos-Hub offers a host-agnostic functional pipeline, Functional 2.0, which interrogates shotgun metagenomic and metatranscriptomic data to understand metabolic and biochemical potential by annotating translated reads with numerous functional databases:

  • MetaCyc Pathways,
  • Enzyme Commissions,
  • Pfam,
  • CAZy,
  • GO Terms.

Abundance normalization (copies per million) ensures comparability across samples with variable depth. With intuitive visualizations and extensive feature descriptions, Functional 2.0 enables users to explore microbial gene function, pathway information, and environmental or health associations with clarity.

Using an in-house algorithm, Functional 2.0 leverages the ever-popular HUMAnN3 framework, but delivering results 19X faster.

Comprehensive metagenomics for planetary microbiomes beyond humans

Functional 2.0 is offered in combination with Kepler™ which combines exact k-mer matching with probabilistic alignment to generate microbiome profiles for bacteria, fungi, viruses & protists from shotgun data.

Kepler™ allows researchers to understand the nearest neighboring reference genome in the database at sub-species level. Its meticulously curated database, GenBook™, and patented algorithm efficiently identify taxa, even in low-biomass or host-contaminated samples. 

Benchmarking studies highlight Kepler™'s superior sensitivity, accuracy, and speed compared to KRAKEN, MetaPhlAn4, and other standard tools, making it ideal for microbiome discovery across clinical, agricultural, and environmental domains.

To learn more, download the whitepaper here: http://www.cosmos-hub.com/content-library

 

 

Powered by the Kepler™ infrastructure, this pipeline uses curated k-mer biomarkers from ResFinder and VFDB to detect antimicrobial resistance (AMR) genes and virulence factors (VFs) directly from raw reads without genome assembly. Its biomarker-based scoring and hierarchical classification enable accurate quantification across classes and genes.

This pipeline is ideal for AMR surveillance, diagnostic microbiology, and functional microbial profiling.

To learn more, download the whitepaper here: http://www.cosmos-hub.com/content-library

Targeted Microbial and Fungal Profiling for Bacteria and Eukaryotes
Our amplicon sequencing workflows provide high-resolution taxonomic profiling of microbial communities using targeted regions—16S rRNA for bacteria and archaea, and ITS for fungi.

  • The short-read 16S pipeline utilizes the DADA2 algorithm for denoising and ASV inference, ensuring genus resolution of bacterial taxa. Taxonomy is assigned using the SILVA database, and community-level functional potential via Metacyc Pathways and Enzyme Commissions is inferred with PICRUSt2.

To learn more about DADA2, see the publication here: https://www.nature.com/articles/nmeth.3869

  • The short-read ITS pipeline is optimized for fungal community profiling, leveraging the QIIME framework along with the UNITE database for closed-reference OTU picking. It processes reads through trimming and merging, outputting tables of OTU IDs, frequencies, and relative abundances.

To learn more, see the publications below:

Emu is a growingly popular tool designed specifically for long-read amplicon data generated by Oxford Nanopore Technologies or Pacific Biosciences instrumentation. It uses probabilistic alignment and relevant references to classify full-length amplicon reads reliably at species-level accuracy, overcoming the resolution and bias limitations of short-read amplicon sequencing approaches.

The Cosmos-Hub iteration of Emu is built with flexibility in mind, allowing users to analyze 16S, ITS, 18S or full 16S-18S-23S full operon data. Additionally, many databases have been implemented to allow users to tailor their analysis to their sample type and study questions:

  • 16S Amplicon: GreenGenes2, SILVA, GreenGenes2, GTDB SSU 220, EMU Default, MIDAS, eHOMD.
  • ITS Amplicon: UNITE
  • 18S Amplicon: SILVA
  • 16S-ITS-23S Full Operon: MirROR v2

Emu has many practical applications including clinical microbiology, environmental & industrial use and is particularly effective with low biomass human microbiome such as breast milk & tissue biopsies, for example.

Learn more about Emu: https://cosmos-hub.com/long-read-amplicon-profiling

Frequently Asked Questions

Want to run a few samples and test the pipelines?

 Contact us below and a member of the team will reach out to arrange a call to discuss your project.