NCBI taxonomy
======

Taxonomic annotation of WoL2 genomes based on NCBI taxdump release 2022-01-01.

 - Source: https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/

Database files:

 - taxid.map: Genome ID to TaxID mapping.
 - nodes.dmp: NCBI taxdump node mapping.
 - names.dmp: NCBI taxdump name mapping.
 - lineages.txt: Lineage strings with taxon names.
 - linetids.txt: Lineage strings with TaxIDs.
 - tax2tree/: Tax2Tree-curated taxonomy.
 - 2022-01-01/: The entire NCBI taxdump (release 2022-01-01).

Notes:

 - The current directory hosts original (uncurated) NCBI annotations.

 - NCBI taxdump contains ranks other than the seven standard ranks, such as
   subspecies, strain and isolate. Theese ranks are not reflected in the
   lineage strings.

 - NCBI taxdump assigns Bacteria and Archaea to rank "superkingdom". They were
   re-assigned to rank code "d" (domain) in the lineage strings.

Protocol:

Taxonomic assignments (TaxIDs) of genomes were adopted from the original
assembly summary (2020-05-14), and manually curated to remove inconsistent
taxonomic assignments to match taxdump (2022-01-01).

 - TaxIDs of 186 genomes were changed.