Package index • dbpq

Download databases

Download latest versions of reference databases.

download_unite_db(): Download a UNITE reference database
download_silva_db(): Download a SILVA reference database NR99 version
download_pr2_db(): Download a PR2 reference database
download_greengenes2_db(): Download a Greengenes2 reference database
download_rdp_db(): Download an RDP reference database
download_midori2_db(): Download a MIDORI2 reference database
download_bold_db(): Download sequences from BOLD Systems
download_diatbarcode_db(): Download a Diat.barcode reference database
download_ksgp_db(): Download the KSGP or GTDB+ reference database
download_ltplus_db(): Download the LTPlus reference database
download_marjaam_db(): Download the MaarjAM reference database
download_eukaryome_db(): Download the Eukaryome reference database

Format taxonomy headers

Convert between taxonomy header formats (SINTAX, UNITE, Greengenes2, dada2).

format_fasta_db(): Convert a FASTA database to a specified taxonomy format
format2dada2(): Format taxonomy headers for dada2::assignTaxonomy
format2dada2_species(): Format taxonomy headers for dada2::addSpecies
format2sintax(): Format taxonomy headers to SINTAX format

Summarize databases

Describe and explore database contents.

count_seq_db(): Count sequences in a FASTA file
count_pattern_db(): Count lines matching a pattern in a FASTA file
count_unwanted_tax(): Count unwanted values in a taxonomy table
list_ranks_db(): List and count taxonomic ranks from a FASTA database
summarize_db(): Summarize a FASTA reference database

Diagnose & profile databases

Check format, integrity, and quality, and profile taxonomic richness and cross-database overlap.

diagnose_db(): Diagnose one or several FASTA reference databases
profile_db(): Profile the taxonomic content of one or several FASTA databases

Taxonomic assignment

Assign taxonomy to sequences.

add_sh_to_taxonomy() experimental: Annotate query sequences with UNITE Species Hypothesis (SH) names

Modify databases

Filter, trim, and transform FASTA databases.

filter_db(): Filter a FASTA database by taxonomic pattern
cutadapt_rm_primers_db(): Remove primers from a FASTA database using cutadapt

Utilities

Helper functions.

get_file_extension(): Get file extension(s)
tax_prefixes(): Get rank information for a taxonomy format
detect_tax_format(): Detect taxonomy format from FASTA headers
is_vsearch_installed(): Check whether vsearch is installed
find_vsearch(): Find the vsearch executable