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:

• QIIME: https://pubmed.ncbi.nlm.nih.gov/24060131/

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, HOMDB.
• ITS Amplicon: UNITE
• 18S Amplicon: SILVA
• 16S-ITS-23S Full Operon: RRN

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.

To learn more about Emu, you can read the publication here: https://pmc.ncbi.nlm.nih.gov/articles/PMC9939874/