The OBITools formatted taxonomy

Management of the taxonomy

Filtering and annotation steps in the processing of DNA metabarcoding sequence data are greatly eased by the explicit association of taxonomic information to sequences together with an easy access to the taxonomy. Taxonomic information, including a taxonomic identifier, can thus be stored in the set of attributes of each sequence record. Specifically, the taxid attribute is used by the OBITools when querying taxonomic information of a sequence record, nevertheless several OBITools commands can annotate sequence records with taxonomy-related attributes for the user’s convenience. The value of the taxid attribute must be a unique integer referring unambiguously to one taxon in the taxonomic associated database (note that a taxon can be any node in the taxonomic tree). Although this is not mandatory, the NCBI taxonomy is a preferred source of taxonomic information as the OBITools provide commands to easily extract the full taxonomic information from it. The command obitaxonomy is useful to build a taxonomic database in the OBITools format from a dump of the NCBI taxonomic database (downloadable at the following URL: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz). Moreover, the obitaxonomy command can enrich an existing taxonomy with private taxa, therefore enabling to associate sequence records to taxa not initially present in the reference taxonomic database. As the OBITools have access to the full taxonomic tree topology, they are able to inform higher taxonomic levels from a taxon identifier (e.g. the family, order, class, phylum, etc. corresponding to a genus) leading to efficient and simple annotation and querying of taxonomic information.