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Assign taxonomy (version 1.9.1.0)

Input fasta file:

Do you want to use a taxonomy reference ?:

Taxon assignment method:

Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query:

Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit:

Number of database hits to consider when making an assignment:

What it does

Contains code for assigning taxonomy, using several techniques.

Given a set of sequences, the program attempts to assign the taxonomy of each sequence.

Currently the methods implemented are assignment with BLAST, the RDP classifier, RTAX, mothur, and uclust. The output of this step is an observation metadata mapping file of input sequence identifiers (1st column of output file) to taxonomy (2nd column) and quality score (3rd column). There may be method-specific information in subsequent columns.

Reference data sets and id-to-taxonomy maps for 16S rRNA sequences can be found in the Greengenes reference OTU builds.

The consensus taxonomy assignment implemented here is the most detailed lineage description shared by 90% or more of the sequences within the OTU (this level of agreement can be adjusted by the user). The full lineage information for each sequence is one of the output files of the analysis. In addition, a conflict file records cases in which a phylum-level taxonomy assignment disagreement exists within an OTU (such instances are rare and can reflect sequence misclassification within the greengenes database).