Using the Hub
About
Cosmos-Hub is an secure AWS-based microbiome analysis platform designed to streamline sequencing data analysis through comprehensive and automated bioinformatics pipelines. The Hub efficiently supports diverse data types, including raw, unassembled sequencing reads (FASTQ files) generated by shotgun metagenomics, metatranscriptomics, and amplicon 16S/ITS (both short-reads and long-reads), delivering precise taxonomic and functional profiling in just hours—not weeks.
Getting Started
New to the platform? Get a brief onboarding here
Bioinformatic Pipelines
Learn about our taxonomic and functional pipelines and the use cases
Uploading Data
Cosmos-Hub accepts raw, unassembled reads (FASTQ) files via multiple methods
Comparative Analysis
Fast and comprehensive cohort analysis with our statistical toolbox
Video Library
Find a number of tutorials and videos to help walk you though the platform
Release Notes
Read the latest updates within the Cosmos-Hub
Contact Support
Reach our full support team for quick responses to your questions or feedback
Download Your Data
Download your raw FASTQ files, profiling data, and comparative analyses
Key Features and Capabilities
- Intuitive User Interface: Effortlessly upload data, manage study metadata, and create virtual cohort analysis with dynamic visualizations
- Comprehensive Data Management: Easily analyze data from 16S rRNA, ITS, shotgun metagenomic, and metatranscriptomic studies
- Metadata Tracking and Cohort Generation: Upload your own metadata to describe samples and generate virtual cohorts for comparative analysis.
- Automated Bioinformatics Pipelines: Process raw FASTQ files directly, delivering taxonomic and functional profiling rapidly and accurately.
- Scalable, Secure Cloud Infrastructure: Hosted on AWS for rapid processing and seamless scalability.
Cosmos-Hub Bioinformatic Pipelines
CHAMP™ | Human Microbiome Profiler
CHAMP™ | Human Microbiome Profiler
Tailored for human-associated microbiome analysis with a proprietary phylogenetic marker-based algorithm to minimize false positives/negatives.Provides multi-kingdom taxonomic profiling informed from real-world human microbiome data, along with functional modules like Gut-Brain/Gut-Metabolic Modules and KEGG pathway outputs.Pita et al. CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome. Frontiers in Microbiology, 2024.
Kepler™ | Host-Agnostic Microbiome Profiler
Kepler™ | Host-Agnostic Microbiome Profiler
Suitable for any sample type, including environmental, agricultural, and animal microbiomes. Using a high-precision k-mer-based identification approach, Kepler supports taxonomic profiling across bacteria, fungi, viruses, and protists, leveraging a database of 150,000 genomes and genes encompassing >30,000 species.Read our whitepaper here: Kepler Benchmarking Whitepaper
Functional | Host-Agnostic Functional Profiling
Functional | Host-Agnostic Functional Profiling
Employs an optimized humann3 framework, which can be used for metagenomic and metatranscriptomic data.Outputs include functional annotations from MetaCyc, GeneOntology (GO), Pfam, CAZy, and EnzymeCommission databases, enabling comprehensive functional analyses across diverse microbial environments.
Kepler AMR/VF | Resistome and Virulome Profiler
Kepler AMR/VF | Resistome and Virulome Profiler
Characterize antimicrobial resistance genes and virulence factors with trusted databases like ResFinder and VFDB.
DADA2 | 16S rRNA ASV Pipeline
DADA2 | 16S rRNA ASV Pipeline
High-resolution bacterial community profiling using the DADA2 ASV algorithm and the SILVA 138 database, providing both taxonomic and predicted functional insights.
QIIME | 16S rRNA OTU Pipeline
QIIME | 16S rRNA OTU Pipeline
Utilizes the QIIME2 framework for clustering sequences based on 97% similarity threshold into Operational Taxonomic Units (OTUs) for taxonomic identification based on the SILVA v138 Database.
QIIME | ITS OTU Pipeline
QIIME | ITS OTU Pipeline
Focuses on fungal communities using Internal Transcribed Spacer (ITS) sequencing with the UNITE database for accurate classification.
Comparative Analysis Visualization & Reporting Module
Comparative Analysis Visualization & Reporting Module
Integrates alpha/beta diversity analyses, differential abundance analyses, and configurable visualizations such as heatmaps, stacked bar charts, PCA, and more, enabling user-friendly interpretation and publication-ready results.
EMU | Long-Read 16S Profiling (August 2025)
COMING SOON Enabling long-read 16S (V1-V8) profiling and analysis.
MetaPhlAn4 | Assembly-Based Microbiome Profiler (TBA)
COMING SOON Enabling assembly-based profiling of metagenomic data.