Download pre-built indexes
Pre-built indexes for all reference databases are available for download. Each compressed archive contains the Kaiju .fmi index file, as well as the corresponding nodes.dmp and names.dmp from the NCBI taxonomy.
See the Quickstart guide for instructions on installing Kaiju and running it with a downloadable index. The README contains more detailed information about the program and the databases.
Files are hosted on Amazon AWS S3 storage through the Open Data Sponsorship Program.
| Database | Date | Archive size (GB) | RAM needed (GB) | HTTPS URL |
|---|---|---|---|---|
| nr | Subset of NCBI BLAST nr database containing Archaea, bacteria and viruses. | |||
| 2023-05-10 | 67 | 177 | .tgz | |
| nr_euk | Like nr, but additionally including fungi and microbial eukaryotes, see taxon list | |||
| 2023-05-10 | 82 | 204 | .tgz | |
| refseq | Protein sequences from genome assemblies of Archaea and bacteria with assembly level "Complete Genome", as well as viral protein sequences from NCBI RefSeq. | |||
| 2023-05-10 | 30 | 87 | .tgz | |
| refseq_nr | Protein sequences from Archaea, bacteria, and microbial eukaryotes from NCBI RefSeq non-redundant protein collection, as well as viral protein sequences from NCBI RefSeq. | |||
| 2023-06-17 | 49 | 116 | .tgz | |
| refseq_ref | Protein sequences from Archaea, bacteria from NCBI RefSeq representative assemblies, as well as viral protein sequences from NCBI RefSeq. | |||
| 2023-07-05 | 31 | 49 | .tgz | |
| progenomes | Representative proteins from proGenomes v3 + viral protein sequences from NCBI RefSeq | |||
| 2023-05-10 | 66 | 102 | .tgz | |
| fungi | Fungi + virus sequences from NCBI RefSeq | |||
| 2023-05-10 | 3.4 | 5 | .tgz | |
| viruses | Viral protein sequences from NCBI RefSeq | |||
| 2023-05-10 | 0.25 | 0.5 | .tgz | |
| plasmids | Plasmid protein sequences from NCBI RefSeq | |||
| 2023-05-10 | 1.4 | 4 | .tgz | |
| rvdb | Protein sequences from RVDB-prot v26.0 | |||
| 2023-05-10 | 16 | 75 | .tgz | |
Older databases are available at the web server page.