Using the Hub
Available Data Workflows
This page describes each of the workflows available in the Cosmos-Hub.
The Cosmos-Hub accepts raw sequencing data produced by Illumina, MGI, Element, Oxford Nanopore, PacBio technologies.
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.
EMU | Long-Read Amplicon Profiling
EMU | Long-Read Amplicon Profiling
Profile long-read 16S/18S/ITS data generated by PacBio or Oxford Nanopore using our customizable EMU pipeline with multi-database support
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.
MetaPhlAn4 | Assembly-Based Microbiome Profiler (TBA)
COMING SOON Enabling assembly-based profiling of metagenomic data.
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.Any raw data after 14 days from upload will be archived in cold storageNew 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.Credits are required to run new workflows on all samples.