Index zone

HTTPS and S3 links to genomic index files freely available in the AWS cloud

Home
Bowtie
HISAT
Kraken/Bracken
Centrifuge
SPUMONI
SPUMONI 2

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: June 2023 update, plus May 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 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.)

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 genomes & taxa are represented.

Collection Contains Date Archive size (GB) Index size (GB) HTTPS URL Inspect
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 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
nt Database Very large collection, inclusive of GenBank, RefSeq, TPA and PDB 5/2/2023 360 480 .tar.gz .txt
EuPathDB462 Eukaryotic pathogen genomes with contaminants removed 4/18/2023 8.4 11 .tar.gz .txt
  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.

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
EuPathDB46 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
3/14/2023            
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 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
12/9/2022            
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 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
9/26/2022            
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 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
6/7/2022            
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 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
5/17/2021            
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
1/27/2021            
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
9/19/2020            
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.

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.