AMPtk Downstream Tools

AMPtk to Phyloseq

Importing a BIOM table from AMPtk into Phyloseq is relatively straightforward:

#load in biom and tree file
physeq <- import_biom('mydata.biom', 'mydata.tree.phy')

#rename taxonomy headings
colnames(tax_table(physeq)) <- c("Kingdom", "Phylum", "Class",
  "Order", "Family", "Genus", "Species")

#print the sample variables


The BIOM file produced by amptk taxonomy is compatible directly with QIIME community ecology scripts, assuming that you have a QIIME compatible mapping file: -i otu_table.biom -o taxa_summary -m mapping_file.txt

AMPtk to Online Tools

The BIOM output is also compatible with Phinch web based visualization as well as MetaCoMET.