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Kraken 2, KrakenUniq and Bracken indexes

Kraken 2 is a fast and memory efficient tool for taxonomic assignment of metagenomics sequencing reads. Bracken is a related tool that additionally estimates relative abundances of species or genera. See the Kraken 2 manual for more information about the individual libraries and their relationship to public repositories like Refseq. See also the Kraken protocol for advice on how to use it.

Kraken 2 / Bracken Refseq indexes

Latest: January 2024 update, plus November 2023 nt addition

Starting Fall 2020, we began creating indexes for more combinations of RefSeq databases. All packages contain a Kraken 2 database along with Bracken databases built for 50, 75, 100, 150, 200, 250 and 300-mers. In some cases (i.e. for collections with “-8” or “-16” in the name) we used the --max-db-size option to cap the size of the database produced. This makes the index smaller at the expense of some sensitivity and accuracy. In all cases we use the defaults for k-mer length, minimizer length, and minimizer spacing.

Starting May, 2023, we began including an index built over the entire nt Database, inclusive of GenBank, RefSeq, TPA and PDB. This is very large! (Hundreds of gigabytes.) We update it when we can; so far, this has been less frequent than our regular quarterly updates. The most recent was on November 29, 2023. We are working on improving the frequency of the nt updates.

Links in the Inspect column are to files containing the output of running kraken2-inspect on the index, giving a quick way of checking what taxa are represented. Similarly, links in the Library column are to library_report.tsv files that give a way to check what sequences were included. The library_report.tsv file lists the sequence IDs from the library FASTA file as well as the URL they came from.

Collection Contains Date Archive size (GB) Index size (GB) HTTPS URL Inspect Library
Viral Refeq viral 1/12/2024 0.5 0.6 .tar.gz .txt .tsv
MinusB Refeq archaea, viral, plasmid, human1, UniVec_Core 1/12/2024 6.7 9.7 .tar.gz .txt .tsv
Standard Refeq archaea, bacteria, viral, plasmid, human1, UniVec_Core 1/12/2024 55 72 .tar.gz .txt .tsv
Standard-8 Standard with DB capped at 8 GB 1/12/2024 5.5 7.5 .tar.gz .txt .tsv
Standard-16 Standard with DB capped at 16 GB 1/12/2024 11 15 .tar.gz .txt .tsv
PlusPF Standard plus Refeq protozoa & fungi 1/12/2024 59 77 .tar.gz .txt .tsv
PlusPF-8 PlusPF with DB capped at 8 GB 1/12/2024 5.5 7.5 .tar.gz .txt .tsv
PlusPF-16 PlusPF with DB capped at 16 GB 1/12/2024 11 15 .tar.gz .txt .tsv
PlusPFP Standard plus Refeq protozoa, fungi & plant 1/12/2024 126 171 .tar.gz .txt .tsv
PlusPFP-8 PlusPFP with DB capped at 8 GB 1/12/2024 5.1 7.5 .tar.gz .txt .tsv
PlusPFP-16 PlusPFP with DB capped at 16 GB 1/12/2024 11 15 .tar.gz .txt .tsv
nt Database Very large collection, inclusive of GenBank, RefSeq, TPA and PDB 11/29/2023 550 710 .tar.gz .txt .tsv
EuPathDB462 Eukaryotic pathogen genomes with contaminants removed 4/18/2023 8.4 11 .tar.gz .txt N/A
  1. Human libraries are created with the --no-mask argument
  2. Index is built using sequences from EuPathDB project, with contamination removed using the method of Lu & Salzberg

Each index includes an inspect.txt file giving the output of the kraken-inspect command.

As of March 2023, each index includes a ktaxonomy.tsv file giving the output of the make_ktaxonomy.py script from KrakenTools.

As of October 2023, each index also includes a library_report.tsv file giving information about the sequences included in the library.

Corresponding S3 URLs can be obtained by removing https://genome-idx.s3.amazonaws.com from the beginning of the URLs linked to above and replacing with s3://genome-idx.

Kraken 2 / Bracken 16s RNA indexes

All packages contain a Kraken 2 database along with Bracken databases built for 100mers, 150mers, and 200mers.

Collection Size (MB) HTTPS URL
Greengenes 13.5 73.2 .tar.gz
RDP 11.5 168 .tar.gz
Silva 132 117 .tar.gz
Silva 138 112 .tar.gz

Corresponding S3 URLs can be obtained by removing https://genome-idx.s3.amazonaws.com from the beginning of the URLs linked to above and replacing with s3://genome-idx.

KrakenUniq indexes

Download both the .tar.gz and database.kdb files to same directory, then expand the .tar.gz file to obtain the full set of files needed for KrakenUniq and Bracken.

Collection Contains Date Index size (GB) HTTPS URL
Standard archaea, bacteria, viral, human, UniVec_Core 6/16/2022 377 .kdb .tar.gz
MicrobialDB archaea, bacteria, viral, human, UniVec_Core, Eukaryotic pathogen genomes with contaminants removed 8/16/2020 384 .kdb .tar.gz

Older Kraken 2 / Bracken Refseq indexes

Collection Contains Date Archive size (GB) Index size (GB) HTTPS URL Inspect Library
October 9, 2023              
Viral Refeq viral 10/9/2023 0.5 0.6 .tar.gz .txt .tsv
MinusB Refeq archaea, viral, plasmid, human1, UniVec_Core 10/9/2023 6.6 9.5 .tar.gz .txt .tsv
Standard Refeq archaea, bacteria, viral, plasmid, human1, UniVec_Core 10/9/2023 53 70 .tar.gz .txt .tsv
Standard-8 Standard with DB capped at 8 GB 10/9/2023 5.5 7.5 .tar.gz .txt .tsv
Standard-16 Standard with DB capped at 16 GB 10/9/2023 11 15 .tar.gz .txt .tsv
PlusPF Standard plus Refeq protozoa & fungi 10/9/2023 57 74 .tar.gz .txt .tsv
PlusPF-8 PlusPF with DB capped at 8 GB 10/9/2023 5.5 7.5 .tar.gz .txt .tsv
PlusPF-16 PlusPF with DB capped at 16 GB 10/9/2023 11 15 .tar.gz .txt .tsv
PlusPFP (ISSUE: see below) Standard plus Refeq protozoa, fungi & plant 10/9/2023 124 148 .tar.gz .txt .tsv
PlusPFP-8 PlusPFP with DB capped at 8 GB 10/9/2023 5.1 7.5 .tar.gz .txt .tsv
PlusPFP-16 PlusPFP with DB capped at 16 GB 10/9/2023 11 15 .tar.gz .txt .tsv
June 5, 2023              
Viral Refeq viral 6/5/2023 0.5 0.6 .tar.gz .txt  
MinusB Refeq archaea, viral, plasmid, human1, UniVec_Core 6/5/2023 6.5 9.4 .tar.gz .txt  
Standard Refeq archaea, bacteria, viral, plasmid, human1, UniVec_Core 6/5/2023 51 67 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 6/5/2023 5.5 7.5 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 6/5/2023 11 15 .tar.gz .txt  
PlusPF Standard plus Refeq protozoa & fungi 6/5/2023 55 71 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 6/5/2023 5.5 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 6/5/2023 11 15 .tar.gz .txt  
PlusPFP (ISSUE: see below) Standard plus Refeq protozoa, fungi & plant 6/5/2023 108 148 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB 6/5/2023 5.1 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 6/5/2023 10 15 .tar.gz .txt  
May 2, 2023              
nt Database Very large collection, inclusive of GenBank, RefSeq, TPA and PDB 5/2/2023 360 480 .tar.gz .txt  
March 14, 2023              
Viral Refeq viral 3/14/2023 0.4 0.5 .tar.gz .txt  
MinusB Refeq archaea, viral, plasmid, human1, UniVec_Core 3/14/2023 6.4 9.0* .tar.gz .txt  
Standard Refeq archaea, bacteria, viral, plasmid, human1, UniVec_Core 3/14/2023 49 64 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 3/14/2023 5.5 7.5 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 3/14/2023 11 15 .tar.gz .txt  
PlusPF Standard plus Refeq protozoa & fungi 3/14/2023 53 69 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 3/14/2023 5.5 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 3/14/2023 11 15 .tar.gz .txt  
PlusPFP (ISSUE: see below) Standard plus Refeq protozoa, fungi & plant 3/14/2023 106 144 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB 3/14/2023 5.1 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 3/14/2023 11 15 .tar.gz .txt  
December 9, 2022              
Viral viral 12/9/2022 0.4 0.5 .tar.gz .txt  
MinusB archaea, viral, plasmid, human1, UniVec_Core 12/9/2022 6.1 8.7 .tar.gz .txt  
Standard archaea, bacteria, viral, plasmid, human1, UniVec_Core 12/9/2022 48 62 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 12/9/2022 5.5 7.5 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 12/9/2022 11 15 .tar.gz .txt  
PlusPF Standard plus protozoa & fungi 12/9/2022 51 66 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 12/9/2022 5.5 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 12/9/2022 11 15 .tar.gz .txt  
PlusPFP (ISSUE: see below) Standard plus protozoa, fungi & plant 12/9/2022 104 142 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB 12/9/2022 5.1 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 12/9/2022 11 15 .tar.gz .txt  
September 26, 2022              
Viral viral 9/8/2022 0.4 0.5 .tar.gz .txt  
MinusB3 archaea, viral, plasmid, human1, UniVec_Core 9/26/2022 5.9 8.5 .tar.gz .txt  
Standard3 archaea, bacteria, viral, plasmid, human1, UniVec_Core 9/26/2022 46 60 .tar.gz .txt  
Standard-83 Standard with DB capped at 8 GB 9/26/2022 5.5 7.5 .tar.gz .txt  
Standard-163 Standard with DB capped at 16 GB 9/26/2022 11 15 .tar.gz .txt  
PlusPF Standard plus protozoa & fungi 9/8/2022 49 64 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 9/8/2022 5.5 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 9/8/2022 11 15 .tar.gz .txt  
PlusPFP (ISSUE: see below) Standard plus protozoa, fungi & plant 9/8/2022 99 129 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB 9/8/2022 5.1 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 9/8/2022 11 15 .tar.gz .txt  
June 7, 2022              
Viral viral 6/7/2022 0.4 0.5 .tar.gz .txt  
MinusB archaea, viral, plasmid, human1, UniVec_Core 6/7/2022 5.8 8.2 .tar.gz .txt  
Standard archaea, bacteria, viral, plasmid, human1, UniVec_Core 6/7/2022 44 58 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 6/7/2022 5.5 7.5 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 6/7/2022 12 15 .tar.gz .txt  
PlusPF Standard plus protozoa & fungi 6/7/2022 47 61 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 6/7/2022 5.2 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 6/7/2022 12 15 .tar.gz .txt  
PlusPFP (ISSUE: see below) Standard plus protozoa, fungi & plant 6/7/2022 55 129 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB 6/7/2022 5.5 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 6/7/2022 11 15 .tar.gz .txt  
May 17, 2021              
Viral viral 5/17/2021 0.4 0.5 .tar.gz .txt  
MinusB archaea, viral, plasmid, human1, UniVec_Core 5/17/2021 5.2 7.5 .tar.gz .txt  
Standard archaea, bacteria, viral, plasmid, human1, UniVec_Core 5/17/2021 38.6 50.1 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 5/17/2021 5.5 7.5 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 5/17/2021 11.2 14.9 .tar.gz .txt  
PlusPF Standard plus protozoa & fungi 5/17/2021 41.0 53.2 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 5/17/2021 5.5 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 5/17/2021 11.2 14.9 .tar.gz .txt  
PlusPFP Standard plus protozoa, fungi & plant (not in this release2; see archive) N/A N/A N/A N/A N/A  
PlusPFP-8 PlusPFP with DB capped at 8 GB 5/17/2021 5.2 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 5/17/2021 10.6 14.9 .tar.gz .txt  
January 27, 2021              
Viral viral 12/2/2020 0.4 0.4 .tar.gz .txt  
MinusB archaea, viral, plasmid, human1, UniVec_Core 12/2/2020 5.1 7.4 .tar.gz .txt  
Standard archaea, bacteria, viral, plasmid, human1, UniVec_Core 12/2/2020 36.0 46.8 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 12/2/2020 5.5 7.5 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 12/2/2020 11.2 14.9 .tar.gz .txt  
PlusPF Standard plus protozoa & fungi (fixed from 12/2/20 version3) 1/27/2021 38.4 49.8 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB (fixed from 12/2/20 version3) 1/27/2021 5.5 7.5 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB (fixed from 12/2/20 version3) 1/27/2021 11.2 14.9 .tar.gz .txt  
PlusPFP Standard plus protozoa, fungi & plant (fixed from 12/2/20 version3) 1/27/2021 71.8 96.3 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB (fixed from 12/2/20 version3) 1/27/2021 5.2 7.5 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB (fixed from 12/2/20 version3) 1/27/2021 10.7 14.9 .tar.gz .txt  
September 19, 2020              
MinusB archaea, viral, plasmid, human1, UniVec_Core 9/19/2020 5.0 7.3 .tar.gz .txt  
Standard archaea, bacteria, viral, plasmid, human1, UniVec_Core 9/19/2020 36.0 47.0 .tar.gz .txt  
Standard-8 Standard with DB capped at 8 GB 9/19/2020 5.5 7.4 .tar.gz .txt  
Standard-16 Standard with DB capped at 16 GB 9/19/2020 11.2 14.9 .tar.gz .txt  
PlusPF Standard plus protozoa & fungi 9/19/2020 37.0 48.0 .tar.gz .txt  
PlusPF-8 PlusPF with DB capped at 8 GB 9/19/2020 5.5 7.4 .tar.gz .txt  
PlusPF-16 PlusPF with DB capped at 16 GB 9/19/2020 11.2 14.9 .tar.gz .txt  
PlusPFP Standard plus protozoa, fungi & plant 9/19/2020 66.5 90.0 .tar.gz .txt  
PlusPFP-8 PlusPFP with DB capped at 8 GB 9/19/2020 5.3 7.4 .tar.gz .txt  
PlusPFP-16 PlusPFP with DB capped at 16 GB 9/19/2020 10.7 14.9 .tar.gz .txt  
  1. The PlusPF database (including PlusPF-8 and PlusPF-16), as well as the PlusPFP database (including PlusPFP-8 and PlusPFP-16) posted on 5/17/2021 mistakenly omitted genomes from Refseq “fungi”. We posted the fixed databases on 1/27 and 1/28/2021.
  2. ISSUE: For several releases from June 2022–October 2023, the full PFP index was distributed with truncated Bracken database files. Correct Bracken database files should be roughly 2–4 MB, but the truncated files were generally in the 10s or 100s of KB in size. Apologies for this error, which went unnoticed for a while. This was resolved as of the January 2024 release.

Older “Minikraken” indexes

The following table points to the “Minikraken” indexes we created initially. All packages contain a Kraken 2 database along with Bracken databases built for 100, 150, and 200-mers. Some also contain Bracken databases for 50, 75 and 250-mers.

Collection Contains Date Archive size (GB) Index size (GB) HTTPS URL
Minikraken v1 Refseq: bacteria, archaea, viral 3/2020 5.6 8 .tar.gz
Minikraken v2 Refseq: bacteria, archaea, viral, human* 3/2020 5.5 8 .tar.gz

Kraken, Kraken 2, Bracken and KrakenUniq are the work of Derrick Wood, Steven Salzberg, Jennifer Lu, Florian Breitwieser, Christopher Pockrandt, Aleksey Zimin, Daniel Baker, Martin Steinegger and Ben Langmead among others. Please see the Kraken, Kraken 2, KrakenUniq and Bracken websites for more information on the software, authors, and how to cite the work.