For 16S rRNA data, there are several pipelines for processing the raw sequence data into an OTU table. For instance,
- QIIME: script make_otu_table.py produces an OTU table in biom format.
- Mothur: commands such as make.shared and make.biom are used to create OTU tables in shared and biom formats respectively.
- UPARSE: an OTU table can be generated using the usearch_global command in biom (QIIME) or shared (mothur) format.
For Shotgun sequencing data, HUMAnN and MG-RAST are the two main platforms that can be used for data annotation to generate a KO count table. More recently, QIIME also offers support for shotgun metagenomics data using their established pipelines (details)