Guides
Guides

Uploading Sequencing Data

Describes the 4 options for uploading metagenomic sequencing data to the CosmosID-HUB

💵

Samples are analyzed on a per-sample fee basis and a credit system

Contact [email protected] for pricing.

Expand the navigation menu by clicking the hamburger icon alt text on upper left side of the screen.

Click "Upload" to navigate to the upload page.

There are 4 options for uploading either single- or paired-end data to the CosmosID-HUB:

Alternatively, if sampels are sequenced with us, we will upload your data files for you and initiate the workflows based on your project.


📘

Accepts both single-end and paired-end data

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 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:
Seqrun1_L001_R1.fastq.gz
Seqrun1_L001_R2.fastq.gz

Seqrun1_R1_001.fastq.gz
Seqrun1_R2_001.fastq.gz



You will then be prompted to:

A. Select your data type

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

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.



B. 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!





C. (Optional) Upload your Metadata

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




D. Select your workflow

Choose the analysis workflow(s) of your liking:

CHAMP™ Human Taxonomic & Functional Microbiome Profiling

Kepler Host-Agnostic Taxonomic Microbiome Profiling

Host-Agnostic Functional Profiling

AMR and Virulence Markers

ASV 16S rRNA Amplicon Profiling

OTU ITS rRNA Amplicon Profiling


E. Click "Start Upload" to upload your samples


❗️

If you use the web GUI for 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.