An overview of how to get started with CosmosID-HUB Microbiome and GenBook™

Welcome to CosmosID-HUB Microbiome! Here we will walk you through everything you need to get started with CosmosID, from creating an account to uploading samples and viewing results. Briefly CosmosID-HUB Microbiome uses raw, unassembled reads as input and matches the sequence against GenBook™, our expertly curated reference database. GenBook™ is derived from private and public databases of assembled genomes and constitutes hundreds of millions of marker sequences representing both coding and non-coding sequences that are shared or uniquely identified across taxonomic or phylogenetic levels. If you would prefer to watch a video that takes you through the entire process, just click here.

In this guide we will go through the following steps:

Create an account and log in
Upload your samples and its associated metadata
Look at your results
Bonus Step
Quick walkthrough of CosmosID-HUB

Step 1 Create An Account or Sign In

Navigate to the following page in your web browser

To create a new account, click "Sign Up" in the center of the log in page:

Follow the field prompts, review the terms of use, and check the box to accept. Click "Sign Up" and you will receive a welcome email.

If you already have an account and would like to sign in, enter your email address and password in the Sign In box. If you have forgotten your password, simply click "Forgot password?" in the Sign In box.


You also can sign in using gmail

Just click the Google Sign In button!


Once you have made a new account on CosmosID-HUB, please reach out to [email protected] to request your free trial

Step 2 Upload Your Samples and Its Associated Metadata


If you don't have fasta/q files to upload, you can skip this step and use Example data.

If you would like to upload samples from Illumina BaseSpace, just click here.

If you would like to upload samples from NCBI SRA, just click here.

Navigate to the upload menu
To expand the navigation menu, click the hamburger icon alt text on upper left side of the screen:

Click "Upload" alt text to navigate to the upload page.

Once on the upload page, you can choose to upload your sequencing data using the desktop or the Illumina BaseSpace Sequence Hub or the NCBI SRA upload functionality. The video down below gives you a quick overview of how the upload process looks like.

A box will open which will allow you to select your sample type:

Select Shotgun Metagenomics, Amplicon 16S, or Amplicon ITS based on the type of analysis you will be performing.

Shotgun Metagenomics - using whole genome shotgun sequencing, the CosmosID algorithms identify microorganisms based on entire genomes represented in our database and in your samples

Amplicon 16S - the amplicon 16S is for bacterial 16S identification. Unlike shotgun metagenomics, amplicon 16S analysis looks only at the relevant bacterial 16S rRNA genes, not the entire genome for identification

Amplicon ITS - the amplicon ITS database is for fungal ITS identification.

You also can select which folder in your account you would like the sample to be placed in.

Next to the sample name you will see the number of credits your account will be charged based on sample name and depth. Shotgun metagenomics samples with less than 0.5 GigaBases of sequence data are considered shallow sequencing samples.

Choose the analysis workflow modules of your liking. You will also have the option to choose up to three workflows according to your analysis objectives.

See the chart below for the amount of credits for different analyses.

TaxaFunctionAMR and Virulence Marker
WGS Deep442
WGS Shallow221
Amplicon 16S1N/AN/A
Amplicon ITS1N/AN/A

Click "Start Upload" to upload your samples.


Troubleshooting Sample Upload Failure

Occasionally a sample will fail to upload. Here are a number of possible causes:

  • Poor internet connection
  • Internet connection interruption
  • Browser closed while uploading

How to troubleshoot:

  • If a sample is not in the proper format or fails to run for another reason, the status will show “failed” and you will not be charged a credit. Try to upload a correctly formatted file.
  • If a sample upload has failed due to connectivity reasons, you can simply retry it.
  • If you continue to experience problems with uploading or with a failed sample, please contact us on the CosmosID-HUB chat or [email protected].

What a failed sample looks like:

Step 3 Relax while your samples automatically run

Step 4 Look at your results

To view results for individual samples, click on the Datasets icon on the left navigation bar and click on your sample name. If needed, use the search bar on the top left to find your sample by name. Check out this video for an example:

For details about samples, visualizations, filtering, changing taxonomic levels, etc., go to View Results.

Step 5 Generate comparatives to discern and visualize taxonomic and functional patterns in your microbiome data

Please go to Create Comparatives to learn how to make comparatives with your data

Bonus Step - Look at Example Datasets

If you would like to play with some data or want to compare your samples to human microbiome project samples, just use the example datasets that we have preloaded into every account.

All the details about the Example datasets can be found here: Definitions

Quick Walkthrough/Demo of CosmosID-HUB

Lastly, here is a video that takes you through the entire process of getting started:

What’s Next

Manage Samples