> ## 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.

# Running Data Workflows

> This page describes each of the workflows available in the Cosmos-Hub.

<Check>
  The Cosmos-Hub accepts raw sequencing data produced by Illumina, MGI, Element, Oxford Nanopore, PacBio technologies.
</Check>

# Cosmos-Hub Bioinformatic Pipelines

Select from the options of pipelines available for shotgun metagenomics, short-read 16S, short-read ITS, and Long-read Amplicon:

<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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## How to Rerun Samples

From the main dashboard, select your sample(s) and press "Run More" in the upper right-hand corner. You will have the option to choose any remaining workflows that have not already been run.

<Warning>
  **Any raw data after 14 days from upload will be archived in cold storage**

  New workflows can be run on any samples, but the raw data files required for new workflows will be archived 14 days after the initial upload date. If you are trying to run new workflows on files older than 14 days, please request a data unarchiving and new workflow request by emailing the name of your samples/folders to [help@cosmos-hub.com](mailto:help@cosmos-hub.com).

  Credits are required to run new workflows on all samples.
</Warning>