Generating OTUs and taxonomy for import into ananke

Generating additional information for import into Ananke

Taxonomic classifications and OTU numbers can be imported into Ananke, but they must be generated from the unique sequence file output from the tabulate subcommand. An example of generating taxonomic classifications from QIIME and OTU clusters from UPARSE is given below.

Taxonomic classifications

assign_taxonomy.py -m rdp -i seq.unique.fasta -o assigned_taxonomy
#  Remove the size information from the classification file
sed -i 's/;size=[0-9]*;//g' assigned_taxonomy/seq.unique_tax_assignments.txt

OTU clusters

An example sing the UPARSE pipeline Makes use of a uclust-to-QIIME conversion script I wrote.

usearch -sortbysize seq.unique.fasta -output seq.unique.sorted.fasta -minsize 2
usearch -cluster_otus seq.unique.sorted.fasta -otus otus.fasta -otu_radius_pct 3
usearch -usearch_global seq.unique.fasta -db otus.fasta -strand both -id 0.97 -uc map.uc -threads 6
mesas-uc2clust -t 6 map.uc seq_otus.txt
sed -i 's/;size=[0-9]*;//g' seq_otus.txt

Importing to time-series database

These files can then be imported into a time-series database HDF5 file with the add taxonomy and add sequence_clusters subcommands:

ananke add taxonomy -i ananke_filtered.h5 -d assigned_taxonomy/seq.unique_tax_assignments.txt
ananke add sequence_clusters -i ananke_filtered.h5 -d seq_otus.txt

This information will now appear in the tables in the ananke-ui package, and allow you to explore your data by OTUs.