Taxonomy formats in reference databases

Reference databases for metabarcoding encode taxonomic information in sequence headers using different conventions. Understanding these formats is essential when downloading databases, running taxonomic classifiers, and summarizing results with dbpq.

Taxonomy format overview

dbpq recognizes five taxonomy formats, grouped into two categories: prefix-based formats (where each rank has a short prefix like k__) and positional formats (where ranks are identified by their position in a semicolon-delimited string).

Prefix-based formats

UNITE format (`k`/`p` prefixes)

Used by: UNITE (general FASTA releases)

Each rank is identified by a two-letter prefix followed by double underscores, separated by semicolons:

>AB123456;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Nectriaceae;g__Fusarium;s__oxysporum
ATCGATCG...

Prefix	Rank
`k__`	Kingdom
`p__`	Phylum
`c__`	Class
`o__`	Order
`f__`	Family
`g__`	Genus
`s__`	Species

SINTAX / UTAX format

Used by: UNITE (SINTAX release), PR2 (UTAX format), MIDORI2 (SINTAX format), Eukaryome (SINTAX format)

Taxonomy is encoded with a tax= prefix, single-letter rank codes followed by colons, separated by commas:

>AB123456;tax=d:Eukaryota,k:Fungi,p:Ascomycota,c:Sordariomycetes,o:Hypocreales,f:Nectriaceae,g:Fusarium,s:Fusarium_oxysporum
ATCGATCG...

This format is used by vsearch --sintax and the original USEARCH UTAX algorithm. Note that SINTAX and UTAX use the same header format despite being different classification algorithms.

Prefix	Rank
`d:`	Domain
`k:`	Kingdom
`p:`	Phylum
`c:`	Class
`o:`	Order
`f:`	Family
`g:`	Genus
`s:`	Species

Greengenes2 format (`d`/`p` prefixes)

Used by: Greengenes2

Similar to the UNITE format but starts with d__ (domain) instead of k__ (kingdom):

>abc123 d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
ATCGATCG...

Prefix	Rank
`d__`	Domain
`p__`	Phylum
`c__`	Class
`o__`	Order
`f__`	Family
`g__`	Genus
`s__`	Species

Positional formats

Some databases use semicolon-separated taxonomy without any prefix. The meaning of each rank is determined by its position in the string. The number of levels varies by database.

For these formats, use rank_position in list_ranks_db() to extract a specific rank by position.

Unprefixed semicolon-delimited (generic)

Used by: SILVA (dada2-formatted), RDP (dada2-formatted)

>Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;
ATCGATCG...

The number of levels depends on the specific training set. The dada2::assignTaxonomy() classifier accepts any number of semicolon-separated levels — with or without prefixes — via the taxLevels argument.

PR2 format (no prefixes, 9 levels)

Used by: PR2 (dada2 format)

PR2 uses 9 taxonomic levels specific to protist taxonomy:

>EU293891.1.1750_U Eukaryota;Archaeplastida;Chlorophyta;Chlorophyta_X;Mamiellophyceae;Mamiellales;Bathycoccaceae;Ostreococcus;Ostreococcus_tauri
ATCGATCG...

Position	Rank
1	Domain
2	Supergroup
3	Division
4	Subdivision
5	Class
6	Order
7	Family
8	Genus
9	Species

Sequence name placement

Beyond taxonomy encoding, formats differ in where the sequence name (accession number, e.g. AB123456) appears in the FASTA header:

Format	Sequence name location	Separator	Example header
UNITE (`k__`)	Between `>` and first `;`	`;`	`>AB123456;k__Fungi;p__Ascomycota;...`
SINTAX / UTAX	Between `>` and `;tax=`	`;tax=`	`>AB123456;tax=d:Eukaryota,k:Fungi,...`
Greengenes2	Between `>` and first space	space	`>abc123 d__Bacteria;p__Pseudomonadota;...`
PR2 (positional)	Between `>` and first space	space	`>EU293891.1.1750_U Eukaryota;Archaeplastida;...`
dada2 (positional)	Last taxonomic level (often species)	`;`	`>Bacteria;Proteobacteria;...;Escherichia`

In prefix-based formats (UNITE, SINTAX, Greengenes2), the sequence name is clearly separated from the taxonomy string. In the dada2 positional format used by SILVA and RDP training sets, there is typically no separate accession number — the header contains only taxonomy, and the deepest level often serves as a sequence identifier.

This distinction matters when converting between formats: conversion functions like format2sintax() and format2dada2() must correctly extract or relocate the sequence name.

Working with taxonomy formats in dbpq

Detecting the format

library(dbpq)

# Auto-detect format from file headers
detect_tax_format("my_database.fasta")
#> "unite", "sintax", "greengenes2", "pr2", or "unknown"

Getting rank information

tax_prefixes() returns rank prefixes (character vector) for prefix-based formats and rank positions (integer vector) for positional formats:

library(dbpq)

# Prefix-based formats
tax_prefixes("unite")
#>     k     p     c     o     f     g     s 
#> "k__" "p__" "c__" "o__" "f__" "g__" "s__"
tax_prefixes("sintax")
#>    d    k    p    c    o    f    g    s 
#> "d:" "k:" "p:" "c:" "o:" "f:" "g:" "s:"
tax_prefixes("greengenes2")
#>     d     p     c     o     f     g     s 
#> "d__" "p__" "c__" "o__" "f__" "g__" "s__"

# Positional format (PR2)
tax_prefixes("pr2")
#>      Domain  Supergroup    Division Subdivision       Class       Order 
#>           1           2           3           4           5           6 
#>      Family       Genus     Species 
#>           7           8           9

Summarizing databases

# UNITE format
summarize_db("unite_database.fasta", tax_format = "unite")

# SINTAX format (UNITE SINTAX, MIDORI2 SINTAX)
summarize_db("midori2_sintax.fasta", tax_format = "sintax")

# Greengenes2 format
summarize_db("greengenes2.fasta", tax_format = "greengenes2")

# PR2 positional format
summarize_db("pr2_database.fasta", tax_format = "pr2")

# Auto-detect format
summarize_db("some_database.fasta", tax_format = "auto")

Listing ranks

# Prefix-based: list phyla in a UNITE-format database
list_ranks_db("database.fasta", rank_prefix = "p__")

# Prefix-based: list phyla in a SINTAX-format database
list_ranks_db("database.fasta", rank_prefix = "p:")

# Using tax_format for convenience (extracts first rank)
list_ranks_db("database.fasta", tax_format = "unite")

# Positional: list genera in a PR2 database (position 8)
list_ranks_db("database.fasta", tax_format = "pr2", rank_position = 8)

# Positional: list phyla in any unprefixed database (position 2)
list_ranks_db("database.fasta", rank_position = 2)

Converting between formats

# UNITE (k__) → SINTAX
format_fasta_db(
  taxnames = "AB123;k__Fungi;p__Ascomycota;c__Sordariomycetes",
  output_format = "sintax"
)
#> [1] "AB123;tax=k:Fungi,p:Ascomycota,c:Sordariomycetes"

# SINTAX → UNITE (k__)
format_fasta_db(
  taxnames = "AB123;tax=k:Fungi,p:Ascomycota,c:Sordariomycetes",
  output_format = "unite"
)
#> [1] "AB123;k__Fungi;p__Ascomycota;c__Sordariomycetes"

# Greengenes2 → dada2
format_fasta_db(
  taxnames = "abc123 d__Bacteria;p__Pseudomonadota;g__Escherichia",
  output_format = "dada2"
)
#> [1] "Bacteria;Pseudomonadota;Escherichia;"

Downloading databases in specific formats

Several databases offer SINTAX-formatted downloads alongside their default format:

download_unite_db(dest_dir = "databases", taxonomic_format = "sintax")
download_pr2_db(dest_dir = "databases", format = "sintax")
download_midori2_db(gene = "CO1", format = "SINTAX")
download_sintax_db(gene = "CO1", format = "SINTAX")

Database formats and classification algorithms

Different taxonomic classifiers expect different input formats. The table below shows which formats work with which classifiers, including those available via MiscMetabar::add_new_taxonomy_pq():

Classifier	Expected format	dbpq download	`add_new_taxonomy_pq()` method
`dada2::assignTaxonomy()`	Any `;`-separated taxonomy	`format = "dada2"`	`method = "dada2"`
`dada2::addSpecies()`	`ID Genus species`	`format = "dada2_species"`	`method = "dada2_2steps"`
`vsearch --sintax`	SINTAX (`tax=`)	`taxonomic_format = "sintax"`	`method = "sintax"`
VSEARCH LCA (`--usearch_global`)	Any FASTA	Any	`method = "lca"`
IDTAXA	Custom training set	Convert with `format2dada2()`	`method = "idtaxa"`
BLASTn	Any FASTA	Any	`method = "blastn"`