OTU clustering
The OTU clustering tool clusters a collection of reads to operational taxonomy units.
To run the tool, go to
Microbial Genomics Module (
) | Metagenomics (
) | Amplicon-based OTU clustering (
) | OTU clustering (
).
The tool aligns the reads to all OTUs to create an "alignment score" for each OTU. If a read cannot be put into an already existing OTU (because there is no single OTU that is similar enough, i.e., within 97% similarity), the algorithm tries to optimize the alignment score by allowing to "cross over" from one database reference to another at a cost (the chimera crossover cost). To speed up the chimera crossover detection algorithm, the read is not aligned to all OTUs but only to some "promising candidates" found via a k-mer search. If the best match that can be constructed has at least one crossover and the "constructed alignment" is at least as good as the "similarity percentage", then the read is being considered chimeric.
By default, the similarity percentage parameter is set to 97% in the OTU Clustering tool. Therefore without the chimera crossover cost, the constructed alignments difference score can only be 3% at most. The smaller the chimeric cost, the more likely it is that a read is deemed chimeric; setting it too high decreases the chimeric detection.
The OTU clustering tool produces several outputs:
- a sequence list of the OTU centroids
- abundance tables with the newly created OTUs and the chimeras. Each table give abundance of the OTU or chimeras at each site, as well as the total abundance for all samples.
- a report that summarizes the results of the OTU clustering
- if the input data is paired-end, a report about the merging of overlapping reads
Subsections
- OTU clustering parameters
- OTU clustering tool outputs
- Visualization of OTU abundance tables
- Importing and exporting OTU abundance tables