Kepler™ delivers strain-level detection of microbial shifts within hours—enabling wastewater operators to proactively maintain biological balance and reduce operational risks.

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.

Emu is a growingly popular tool designed specifically for long-read amplicon data generated by Oxford Nanopore Technologies or Pacific Biosciences instrumentation. 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

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.

• 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.