> ## Documentation Index
> Fetch the complete documentation index at: https://docs.cosmosid.com/llms.txt
> Use this file to discover all available pages before exploring further.

# About

<img src="https://mintcdn.com/cmbio/1bkEKvEMzn3OLKqg/logo/dark.svg?fit=max&auto=format&n=1bkEKvEMzn3OLKqg&q=85&s=d0761cd0ad078897e0e627c55375d649" alt="Dark Sv" style={{ width:"52%" }} className="mx-auto" width="2134" height="667" data-path="logo/dark.svg" />

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 **<u>shotgun metagenomics</u>**, **<u>metatranscriptomics</u>**, and **<u>amplicon 16S/ITS</u>** (*both short-reads and long-reads*), delivering precise taxonomic and functional profiling in just hours—not weeks.

<CardGroup cols={2}>
  <Card title="Getting Started" icon="info" iconType="regular" horizontal href="https://docs.cosmosid.com/docs/quick-start">
    New to the platform? Get a brief onboarding here
  </Card>

  <Card title="Bioinformatic Pipelines" icon="gear" horizontal href="https://docs.cosmosid.com/docs/workflows">
    Learn about our taxonomic and functional pipelines and the use cases
  </Card>

  <Card title="Uploading Data" icon="upload" horizontal href="https://docs.cosmosid.com/docs/sample-upload">
    Cosmos-Hub accepts raw, unassembled reads (FASTQ) files via multiple methods
  </Card>

  <Card title="Comparative Analysis" icon="code-compare" horizontal href="https://docs.cosmosid.com/docs/new-comparative-analysis">
    Fast and comprehensive cohort analysis with our statistical toolbox
  </Card>

  <Card title="Video Library" icon="video" horizontal href="https://docs.cosmosid.com/docs/video-library">
    Find a number of tutorials and videos to help walk you though the platform
  </Card>

  <Card title="Release Notes" icon="pen-clip" horizontal href="https://docs.cosmosid.com/docs/updates">
    Read the latest updates within the Cosmos-Hub
  </Card>

  <Card title="Contact Support" icon="envelope" horizontal href="https://cosmos-hub.com/support">
    Reach our full support team for quick responses to your questions or feedback
  </Card>

  <Card title="Download Your Data" icon="download" horizontal href="https://docs.cosmosid.com/docs/download-your-raw-fastqs">
    Download your raw FASTQ files, profiling data, and comparative analyses
  </Card>
</CardGroup>

# **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

<AccordionGroup>
  <Accordion title="CHAMP™ | Human Microbiome Profiler" icon="person-dress">
    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**](https://doi.org/10.3389/fmicb.2024.1425489). Frontiers in Microbiology, 2024.
  </Accordion>

  <Accordion title="Kepler™ | Host-Agnostic Microbiome Profiler" icon="pig">
    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](https://hubs.ly/Q03cpmlN0)
  </Accordion>

  <Accordion title="Functional | Host-Agnostic Functional Profiling" icon="gear-complex-code">
    Employs an optimized humann3 framework, which can be used for metagenomic and metatranscriptomic data.

    Outputs include functional annotations from [MetaCyc](https://metacyc.org/), [GeneOntology (GO)](https://geneontology.org/), [Pfam](http://pfam.xfam.org/), [CAZy](https://www.cazy.org/), and [EnzymeCommission](https://enzyme.expasy.org/) databases, enabling comprehensive functional analyses across diverse microbial environments.
  </Accordion>

  <Accordion title="Kepler AMR/VF | Resistome and Virulome Profiler" icon="mask-face">
    Characterize antimicrobial resistance genes and virulence factors with trusted databases like ResFinder and VFDB.
  </Accordion>

  <Accordion title="EMU | Long-Read Amplicon Profiling" icon="book">
    Profile long-read 16S/18S/ITS data generated by PacBio or Oxford Nanopore using our customizable EMU pipeline with multi-database support
  </Accordion>

  <Accordion title="DADA2 | 16S rRNA ASV Pipeline" description=" " icon="dna">
    High-resolution bacterial community profiling using the DADA2 ASV algorithm and the SILVA 138 database, providing both taxonomic and predicted functional insights.
  </Accordion>

  <Accordion title="QIIME | 16S rRNA OTU Pipeline" icon="right-long-to-line">
    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.
  </Accordion>

  <Accordion title="QIIME | ITS OTU Pipeline" icon="mushroom">
    Focuses on fungal communities using Internal Transcribed Spacer (ITS) sequencing with the UNITE database for accurate classification.
  </Accordion>

  <Accordion title="Comparative Analysis Visualization & Reporting Module" icon="code-compare">
    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.
  </Accordion>
</AccordionGroup>

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# Access and Pricing

The Cosmos-Hub is available to any researchers with access to a web browser.

We offer *monthly and yearly subscription model* with per-sample analysis charges depending on the data type.

There are flexible options with a number of modules to suit your analysis needs, as well as academic pricing. Contact [info@cosmos-hub.com](mailto:info@cosmos-hub.com) for more info.

# [Request a 14 day free trial!](https://cosmosidhub.com/book-a-demo/)