Assign Taxonomies to Sequences in Abundance Table

The Assign Taxonomies to Sequences in Abundance Table tool lets you add taxonomies to abundance table features that have sequences associated. This is useful for annotating amplicon sequence variant (ASV) tables, and OTU tables with de novo OTUs where sequences are not annotated by the initial analysis tools.

The tool requires a reference index and works by mapping each sequence from the abundance table to this reference index. The underlying analysis is the same as for Taxonomic Profiling, see Taxonomic Profiling.

Creating the required reference index

You create a reference index using Create Taxonomic Profiling Index, see Create Taxonomic Profiling Index. As input, you will need a reference database, i.e. a sequence list containing reference sequences with taxonomy annotations.

Reference database can be obtained using one of the Download Database tools. The choice of reference database depends on your data.

For amplicon data, consider the reference databases available with Download Amplicon-Based Reference Database, see Download Amplicon-Based Reference Database.

For whole genome data, you may use the databases from Download Curated Microbial Reference Database, see Download Curated Microbial Reference Database. Alternatively, create your own reference database with Download Custom Microbial Reference Database, see Download Custom Microbial Reference Database.

Running the tool

To run the Assign Taxonomies to Sequences in Abundance Table tool:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Abundance Analysis (Image abundance_folder_closed_16_n_p) | Assign Taxonomies to Sequences in Abundance Table (Image assign_taxo_to_ab_table_16_n_p)

Select the abundance table with sequences to be annotated.

Select the reference index to map the abundance table sequences to (figure 6.5).

Choose settings for taxonomic assignment:

Image assigntaxonomysettings
Figure 6.5: Select reference index and set parameters for taxonomic assignment.

Select Create Report to generate a report with summary information on taxonomic assignment.

The output