General prokaryote and eukaryote Kraken2 database

Database description

Kraken2 database containing all NCBI RefSeq “Complete genome” entries (database accessed on the 11th of February 2021) with accession prefixes NC, NW, AC, NG, NT, NS, and NZ of the following taxonomic groups: archaea, bacteria, fungi, human, protozoa, and viruses. This database also contained a selection of metazoan model species reference genomes, listed below.

Species

Accession

Aedes aegypti

GCF_002204515

Aedes albopictus

GCF_006496715

Anas platyrhynchos

GCF_015476345

Stomoxys calcitrans

GCF_001015335

Apis mellifera

GCF_003254395

Bos taurus

GCF_002263795

Capra hircus

GCF_001704415

Cavia porcellus

GCF_000151735

Chlorocebus sabaeus

GCF_015252025

Columba livia

GCF_000337935

Culex quinquefasciatus

GCF_015732765

Equus caballus

GCF_002863925

Gallus gallus

GCF_000002315

Homo sapiens

GCF_000001405

Ixodes scapularis

GCF_002892825

Meleagris gallopavo

GCF_000146605

Mesocricetus auratus

GCF_000349665

Mus musculus

GCF_000001635

Numida meleagris

GCF_002078875

Ovis aries

GCF_002742125

Rattus norvegicus

GCF_015227675

Sus scrofa

GCF_000003025

Database reconstruction

To reconstruct the database, extract the taxonomy.tar.gz archive as follows:

tar -xvzf taxonomy.tar.gz

the hash.k2d file has been compressed, to decompress it, use the following command:

gunzip --remove hash.k2d.gz

taxonomy.tab contains the required taxonomy information to visualize Kraken2 results with Krona.