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 
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.gzSeqrun1_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.
Updated about 1 month ago