Samples for metagenomic analysis are whole genome shotgun sequencing files - usually fastq or fasta files.
Paired end files can be combined into one sample upon upload as long as they are uploaded together. See Upload Samples & Analyze Samples for more details on how to run your samples.
After upload, CosmosID automatically analyzes your samples. The results include tables and visualizations for our genome databases: bacteria, fungi, protista, viruses, and respiratory viruses, and for our gene databases: antimicrobial resistance and virulence factors.
An extensive academic study shows CosmosID's “Best in Class Accuracy” and “Unrivaled Detection Resolution”. As shown in the figures below, CosmosID clearly offers the best identification accuracy for the entire benchmarking dataset based on F1, precision, recall, and AUPR. Most importantly, unlike other tools, identification accuracy is maintained at all taxonomic levels. Strikingly, most of the tools grossly fall short in classifying organisms at sub-species (and strain) level resolution, but CosmosID provided unrivaled accuracy at sub-species level.
Updated about 3 years ago