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.