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

1. Click "Upload from your computer" within the Upload Menu

From anywhere on the app, you can expand the navigation menu by clicking on the hamburger icon on the upper left side of the screen and click "Upload" to navigate to the upload page.

Click "Upload from your computer" to launch the drag-and-drop menu.

2. Drag-and-drop your files or click to open the file explorer

Once on the upload page, either drag and drop your files or click to open your file browser and select your samples that you would like to upload.

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

📘

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 similarly-named fastq files and with "_R1" or "_R2" followed by either "_001", "_002", etc. followed by the sequencing suffix.

Examples of acceptable paired end names:
Seqrun1_L001_R1.fastq.gz
Seqrun1_L001_R2.fastq.gz

Seqrun1_R1_001.fastq.gz
Seqrun1_R2_001.fastq.gz

If the paired-end files have been named appropriately, the sample will show up as "Paired-read sample" with a single name for each paired-end sample.

If paired-end samples are not named correctly, they will populate as individual "Single-read sample" for each R1/R2. Please delete these samples and check your naming structure before re-selecting samples.

3. Select your desired folder location and data type

NOTE: Folders must be pre-generated in the "Cohorts and Metadata" menu before uploading samples. You can also upload to the /Home folder and move the samples into subfolders after upload.

You are required to select the TYPE of data from the following options:

• 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. This option requires the primer sequences used for generating libraries (e.g,. V1V2, V3V4, V4).
  • You can select from standard primer sequences or input your own primer sequence
• Amplicon ITS - the amplicon ITS database is for fungal ITS identification.

3. Remove host reads

Selecting the sample host can remove host-reads for increased precision and accuracy in microbiome analysis, especially for functional profiling. You can select from various hosts, from humans to domestic cats!

📘

If running CHAMP Human Profiler:

Select "None" as the host when running the CHAMP Human Microbiome Profiler. CHAMP has a native host-removal algorithm for removing human host reads, and selecting a host for this pipeline will result in the sample analysis failing.

4. Upload your Metadata (Optional)

Upload your metadata through a CSV template. This can also be skipped and performed after data upload.

5. Select your workflow

The HUB has several workflows to chose from when uploading your samples:

Shotgun Metagenomic Data

CHAMP™ Human Taxonomic & Functional Microbiome Profiling

Kepler Host-Agnostic Taxonomic Microbiome Profiling

Host-Agnostic Functional Profiling

AMR and Virulence Markers (module required)

Amplicon Data

ASV 16S rRNA Amplicon Profiling

OTU ITS rRNA Amplicon Profiling

Credit charges are assessed upon successful upload and analysis based on the data type. The CosmosID-HUB team will assign you with the correct number of credits according to your subscription terms.

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

6. Click "Start Upload" to upload your samples

Once uploaded, you can view the status of your analysis using the status indicator next to the samples in the Cohorts and Metadata Menu.

❗️

When uploading local files, please do not close or logout from your web browser during the uploading progress. You can find the upload status with the popup in the bottom right hand corner.

Samples will appear in the Cohorts and Metadata menu once uploaded, with a status icon indicating the analysis status.

Please allow up to 24 hours for processing.

🚧

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]