Upload Samples

How to upload samples to CosmosID for analysis

Here we will take you through the process of uploading your samples. After upload, analysis will begin automatically.

1. Navigate to the Upload Page

From anywhere on the app, you can expand the navigation menu by clicking on the hamburger icon alt texton the upper left side of the screen.

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

2. Upload Your Samples Based on Analysis Type

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.

File formats accepted include fasta, .fna, .fasta.gz, .fastq, .fq, .fastq.gz, bam, bam.gz, sra, sra.gz

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 Deep *442
WGS Shallow 221
Amplicon 16S 1N/AN/A
Amplicon ITS1N/AN/A

Click "Start Upload" to upload your samples.


Paired End Files

To upload paired end files, be sure to select them or drag and drop them together (at the same time). You will then be prompted to confirm the pairs so they can be combined for analysis.

Paired End File Naming

Paired end files must be fastq files and named with "_R1" or "_R2" followed by either "_001", "_002", etc. followed by the sequencing suffix (.fastq only).

Examples of acceptable paired end names:



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

Other notes:

  • If a sample fails to upload, you can retry it
  • 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.
  • If you have problems uploading or with a failed sample, please contact us on the app chat or [email protected]

What a failed sample looks like:

What’s Next