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The OBITools formatted taxonomy
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Management of the taxonomy
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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.
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