Core Functionalities

Flexible Raw Data Upload

Upload single- or paired-end FASTQ files by drag-and-drop functionality and BaseSpace integration.

Create your Microbiome Databank

Describe your samples using centralized metadata variables that can enable cohort comparisons and cross-study analysis

Archived and Encrypted Storage Hub

For raw fastqs, profilng results, and metadata

Import Public Datasets

Seamless importing of sequencing data from NCBI’s Sequence Read Archive (SRA) to enable meta-analysis of published data or to revisit your past projects

Remove Host Interference

With automated removal of host reads from raw sequencing reads

Precision Filters for Confidence

Advanced machine learning filters for differentiating signal from noise, as demonstrated in various third-party challenges, meaning that the results are less impacted by false positives.

Suite of Comparative Analysis Tools

Compare diversity, abundance, and more between sample cohorts with statistics and interactive/exportable charts and visualizations

Save time

With pipelines up to 19x faster than open-source tools and automated figures and statistics

1. Unrivalled Bioinformatics Pipelines

Achieve unparalleled insight in microbiome exploration with high resolution, multi-kingdom and functional profiling. Bioinformatics pipelines hosted in the HUB have been validated and benchmarked to deliver the highest levels of recall & precision, in a matter of minutes. Read more about this here.

2. Centralized Data Storage

CosmosID-HUB provides easy upload and centralized storage of raw sequencing data, profiling results and your study metadata, all in one place. From there, you can leverage your metadata to run comparative analyses in just a few clicks.

3. Comparative Analysis Suite

Leverage your metadata to create ad-hoc comparative analyses with any of of the 10+ databases we have available to:


– Look for specific taxa or genes using the matrix table search function

– Monitor the abundance distribution of specific taxa or pathways

– Observe trends across your cohorts and time points with high-resolution heatmaps and stacked bar charts 

– Investigate PCA, Alpha & Beta diversity plots in 2D and 3D

– Test for significance and generate P values for all analyses

– Run differential abundance analysis testing

"Aside from the excellent quality of sequencing data CosmosID generates, their project management skills are exceptional. Our group has benefited immensely from CosmosID’s personalized service and flexibility to work under tight timelines – in past few months, which have brought new challenges to all, CosmosID have helped us regain the pace of our translational microbiome studies. Their user interface for data analysis is also a great tool for teams that need bioinformatic and analytic support."
Jennifer Wargo
MD Anderson Cancer Center
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