The CosmosID Developer Hub

Welcome to the CosmosID developer hub. You'll find comprehensive guides and documentation to help you start working with CosmosID as quickly as possible, as well as support if you get stuck. Let's jump right in!

Get Started    

Quickstart

An overview of how to get started with CosmosID

Welcome to CosmosID! Here we will walk you through everything you need to get started with CosmosID, from creating an account to uploading samples and viewing results. 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
Relax
Look at your results

Step 1 Create An Account or Sign In

Navigate to the following page in your web browser
https://app.cosmosid.com

To create a new account, click "Create Account" in the upper right corner of the log in page:

Enter your email address and create a password. Review the terms of use and check the box to accept. Click "Register" 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 alt text button and sign in using your gmail account.

Free Credits

You will receive 12 free credits when you sign up for CosmosID. These credits allow you to run 12 whole genome shotgun samples or 24 16S samples. The credits will be in your account automatically when you sign in for the first time.

Step 2 Upload Your Samples

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

If you would like to load samples from BaseSpace, 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, either drag and drop your files or click the page to open your file browser and select your samples that you would like to upload.

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.

Select your sample type:

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 5 GigaBases of sequence data are considered shallow sequencing samples and require 2 credits whereas those with more than 5 Gigabases of sequence data require 4 credits. Amplicon samples are 1 credit.

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 app chat or support@cosmosid.com.

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.

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

Video of the Quickstart Process

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

Updated 5 months ago


What's Next

Manage Samples

Manage Samples

Quickstart


An overview of how to get started with CosmosID

Suggested Edits are limited on API Reference Pages

You can only suggest edits to Markdown body content, but not to the API spec.