All pipelines are optimized for short-read data but can accept any sequencing data agnostic of platform:

• Illumina
• MGI
• Element
• Oxford Nanopore
• PacBio

Pipelines

1. CHAMP™ Human Microbiome Profiler
   1. Tailored for human-associated microbiome analysis with a proprietary phylogenetic marker-based algorithm to minimize false positives/negatives.
   2. 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.
2. Kepler™ Host-Agnostic Microbiome Profiler
   1. Suitable for environmental, agricultural, and animal microbiomes using a high-precision k-mer-based identification approach.
   2. Supports taxonomic profiling across bacteria, fungi, viruses, and protists, leveraging a database of 150,000 genomes and genes encompassing >30,000 species.
3. Host-Agnostic Functional Profiling
   1. Employs an optimized HUMANN3 framework, which can also be used for metagenomic and metatranscriptomic data.
   2. Outputs include functional annotations from MetaCyc pathways, GO terms, Pfam, CAZy, and Enzyme Commission. This enables robust functional analysis, enriching insights into microbial functions across diverse environments and hosts.
4. Kepler™ Resistome & Virulome Profiler
   1. Focuses on characterizing antimicrobial resistance genes and virulence factors using ResFinder and VFDB databases.
5. 16S rRNA Amplicon Profiler
   1. Provides high-resolution bacterial community profiling using the DADA2 ASV algorithm and the SILVA 138 database, with taxonomic and predicted functional outputs.
6. ITS Amplicon Profiler
   1. Focuses on fungal communities using Internal Transcribed Spacer (ITS) sequencing with the UNITE database for accurate classification.
7. Comparative Analysis Visualization & Reporting Module
   1. 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.

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.

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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 [email protected].

Credits are required to run new workflows on all samples.