Bioinformatics ServicesAmplicon Analysis


At CosmosID, we leverage our expertise in database curation to build a quality-controlled OTU database for both 16S and ITS amplicon sequencing using a range of open-source databases. Combined with the CosmosID Metagenomics Cloud, microbiome scientists can now can amplicon analysis in a matter of minutes, complete with charts and visualizations which are ready to export!

Amplicon AnalysisHow does it work?

Methods: The CosmosID 16S data analysis pipeline starts with preprocessing of the raw reads from either paired-end or single-end fastq files through read trimming to remove adapters as well as reads and bases of low quality. If the reads are in paired-end format, the forward and reverse overlapping pairs are joined together; the unjoined R1 and R2 reads are then added to the end of the file. The file is then converted to fasta format and used as input for OTU picking. OTUs are identified against the CosmosID curated 16S database using a closed-reference OTU picker and 97% sequence similarity through the QIIME framework. The final results are then presented in tabular format with the taxonomic names, OTU ids, frequency, and relative abundance. Results can be downloaded, or compared to other 16S samples for visualizations through the CosmosID Metagenomics Cloud.

Amplicon AnalysisWhat is the CosmosID-Hub?

Software developers at CosmosID have automated the Amplicon analysis pipeline and made it available through a user-friendly and interactive web-based application which means that you can start analysing your data regardless of how much computational infrastructure you have available to you!

The CosmosID-Hub features:

  • Genus to species-level identification for Bacteria & Fungi

  • Exportable abundance values, charts & visualizations including sunburts, bubble charts & stacked bar graphs

  • Unlimited use of comparative analysis software, complete with Heatmaps, 3D PCA, Alpha Diversity plots & Beta Diversity PCoA

How do I get started?

No licensing or subscription required! Simply send us your samples and the analysis will be completed for you as part of the service or if you have data ready, purchase your credits, upload your data and unlock the microbiome!


Amplicon AnalysisFrequently Asked Questions

What databases are used for 16S analysis?

Similarly to shotgun metagenomics, CosmosID also has a curated OTU database including data from Greengenes and SILVA, for example. For more information on this, please visit the app documentation.

How much does it cost to upload samples onto the hub for analysis?

If you already have completed amplicon sequencing, to upload 16S/ITS data for direct analysis on the metagenomics hub, pricing starts at just$25 USD (1 credit) per sample. This is a one-off cost and indefinite access to the hub is then provided.

Can I use the hub for publication purposes?

Absolutely! Data and visualizations can be exported directly from the hub and publication-ready methods can be provided to help expedite the publication process.