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Samples are analyzed on a per-sample basis, and uploading requires pre-purchased sample credits. Contact info@cosmos-hub.com for pricing.

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There are 4 upload methods to choose from:

Upload from your Computer

Upload local FASTQ, SRA, or BAM files via drag-and-drop.

Link a BaseSpace Account

Connect your Illumina BaseSpace account and import data directly.

Import from NCBI SRA

Use public SRA accession numbers to fetch data.

Use the Command Line Interface

Use our CLI or API for large batch uploads and automation.(Click for API documentation)

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Select Your Data Type

Amplicon pipelines are used to identify bacterial or fungal communities based on specific genes. These workflows support both single-end and paired-end reads.

Requirements

  • Read type: Paired-end or single-end
  • Min samples: 10 (for ASV/DADA2 workflows)
  • File size: ≤ 1 GB uncompressed (250 MB compressed)
  • PHRED score ≥ 20
  • Formats: .fastq.gz, .fq.gz, .fasta.gz, .sra.gz
  • Paired-end naming:
    • SampleID_R1_001.fastq.gz
    • SampleID_R2_001.fastq.gz
  • Reads must overlap ≥ 15 bp
  • Watch the 16S Tutorial Video

Workflow Options

  • ASV 16S rRNA Profiling (DADA2-based)
  • OTU ITS rRNA Profiling (QIIME2-based)

Common Pitfals

  • Filenames with spaces or special characters will break pairing
  • Unpaired files will appear as “Single-read samples”

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Uploading Metadata

You can upload a metadata CSV during or after your data upload through the Cohorts and Metadata page.
Metadata Upload

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Workflow Selection

After upload, choose a workflow that matches your data type. The Cosmos-Hub will only show valid options based on your selections.
Workflow Selection
Do not close your browser while uploading. Progress is shown in the bottom-right. Allow up to 24 hours for processing. Results and statuses will appear in the Cohorts and Metadata section.
Occasionally a sample will fail to upload. Here are a number of possible causes:
  • Poor internet connection
  • Internet connection interruption
  • Browser closed while uploading
  • Incorrect primer pairs
  • Corrupted or low quality data files
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 credits.
  • If you have problems uploading or with a failed sample, please submit a help ticket or email us at help@cosmos-hub.com.