How can I format my data into an acceptable input for MicrobiomeAnalyst?

For 16S rRNA data, there are several pipelines for processing the raw sequence data into an OTU table. For instance,

  • QIIME: script 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)