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!
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.
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
CosmosID’s proficiency in amplicon analysis is unparalleled, making it a trusted choice for many researchers worldwide. Our robust pipeline allows us to handle raw sequencing data from amplicon sequencing services with ease and precision. One of our key starting points is the DNA extraction, a crucial step in sample preparation that allows us to accurately examine environmental samples.
Once we have the data, our experts begin processing amplicon data, focusing on the variable regions. These are the parts of the 16S rRNA gene that contain the greatest species-specific differences and are best for distinguishing among species. We then compare these regions to our comprehensive reference database, which is constantly updated to ensure accuracy.
The output from our bioinformatics analysis is a detailed report with insights into the relative abundance of different species within your sample. We provide a statistical analysis of the microbial communities revealed by 16S rRNA sequencing, assisting you in understanding the full scope of your data.
At CosmosID, we don’t just deliver data; we provide meaningful insights that drive impactful discoveries. Choose CosmosID for your amplicon analysis needs, and let’s explore the microbial universe together.
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!
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.
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.
Absolutely! Data and visualizations can be exported directly from the hub and publication-ready methods can be provided to help expedite the publication process.