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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: April 2025 update

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 September, 2024, we include the new “core_nt” database. This is larger than the Refseq databases and we update it when we can; so far, this has been less frequent than our regular quarterly updates. We are working on improving the frequency of the core_nt updates. We no longer build the older and bigger nt database.

Starting December, 2024, we added a new index for the latest GTDB release, which spans bacteria and archaea. The GTDB team updates this collection approximately annually.

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	MD5
Viral	Refeq viral	4/2/2025	0.5	0.6	.tar.gz	.txt	.tsv	.md5
MinusB	Refeq archaea, viral, plasmid, human¹, UniVec_Core	4/2/2025	7.5	10.6	.tar.gz	.txt	.tsv	.md5
Standard	Refeq archaea, bacteria, viral, plasmid, human¹, UniVec_Core	4/2/2025	66.9	86.8	.tar.gz	.txt	.tsv	.md5
Standard-8	Standard with DB capped at 8 GB	4/2/2025	5.5	7.5	.tar.gz	.txt	.tsv	.md5
Standard-16	Standard with DB capped at 16 GB	4/2/2025	11.2	14.9	.tar.gz	.txt	.tsv	.md5
PlusPF	Standard plus Refeq protozoa & fungi	4/2/2025	71.8	93.2	.tar.gz	.txt	.tsv	.md5
PlusPF-8	PlusPF with DB capped at 8 GB	4/2/2025	5.5	7.5	.tar.gz	.txt	.tsv	.md5
PlusPF-16	PlusPF with DB capped at 16 GB	4/2/2025	11.2	14.9	.tar.gz	.txt	.tsv	.md5
PlusPFP	Standard plus Refeq protozoa, fungi & plant	4/2/2025	147.4	199.6	.tar.gz	.txt	.tsv	.md5
PlusPFP-8	PlusPFP with DB capped at 8 GB	4/2/2025	5.2	7.5	.tar.gz	.txt	.tsv	.md5
PlusPFP-16	PlusPFP with DB capped at 16 GB	4/2/2025	10.5	14.9	.tar.gz	.txt	.tsv	.md5
core_nt Database	Very large collection, inclusive of GenBank, RefSeq, TPA and PDB	12/28/2024	183.0	238.2	.tar.gz	.txt	.tsv	.md5
EuPathDB46²	Eukaryotic pathogen genomes with contaminants removed	4/18/2023	8.4	11	.tar.gz	.txt	N/A	N/A
GTDB v220 (`genomic_files_reps`)	Bacterial and archaeal	12/13/2024	387	497	.tar.gz	.txt	.tsv	.md5

Human libraries are created with the --no-mask argument
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.

As of June 2024, each index also includes a .md5 file that lists checksums for files in the archive.

As of September, 2024, indexes also include names.dmp and nodes.dmp files to the index archives so as to preserve information about the taxonomy used.

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 (EuPathDB54) with contaminants removed	8/8/2023	535	.kdb .tar.gz

Older Kraken 2 / Bracken Refseq indexes

Collection	Contains	Date	Archive size (GB)	Index size (GB)	HTTPS URL	Inspect	Library	MD5
December, 2024
Viral	Refeq viral	12/28/2024	0.5	0.6	.tar.gz	.txt	.tsv	.md5
MinusB	Refeq archaea, viral, plasmid, human¹, UniVec_Core	12/28/2024	7.4	10.5	.tar.gz	.txt	.tsv	.md5
Standard	Refeq archaea, bacteria, viral, plasmid, human¹, UniVec_Core	12/28/2024	64.7	84.1	.tar.gz	.txt	.tsv	.md5
Standard-8	Standard with DB capped at 8 GB	12/28/2024	5.5	7.5	.tar.gz	.txt	.tsv	.md5
Standard-16	Standard with DB capped at 16 GB	12/28/2024	11.2	14.9	.tar.gz	.txt	.tsv	.md5
PlusPF	Standard plus Refeq protozoa & fungi	12/28/2024	69.5	90.5	.tar.gz	.txt	.tsv	.md5
PlusPF-8	PlusPF with DB capped at 8 GB	12/28/2024	5.5	7.5	.tar.gz	.txt	.tsv	.md5
PlusPF-16	PlusPF with DB capped at 16 GB	12/28/2024	11.2	14.9	.tar.gz	.txt	.tsv	.md5
PlusPFP	Standard plus Refeq protozoa, fungi & plant	12/28/2024	143.5	195.2	.tar.gz	.txt	.tsv	.md5
PlusPFP-8	PlusPFP with DB capped at 8 GB	12/28/2024	5.2	7.5	.tar.gz	.txt	.tsv	.md5
PlusPFP-16	PlusPFP with DB capped at 16 GB	12/28/2024	10.5	14.9	.tar.gz	.txt	.tsv	.md5
September, 2024
Viral	Refeq viral	9/4/2024	0.5	0.6	.tar.gz	.txt	.tsv	.md5
MinusB	Refeq archaea, viral, plasmid, human¹, UniVec_Core	9/4/2024	7.3	10.3	.tar.gz	.txt	.tsv	.md5
Standard	Refeq archaea, bacteria, viral, plasmid, human¹, UniVec_Core	9/4/2024	62	80	.tar.gz	.txt	.tsv	.md5
Standard-8	Standard with DB capped at 8 GB	9/4/2024	5.5	7.5	.tar.gz	.txt	.tsv	.md5
Standard-16	Standard with DB capped at 16 GB	9/4/2024	11	15	.tar.gz	.txt	.tsv	.md5
PlusPF	Standard plus Refeq protozoa & fungi	9/4/2024	66	86	.tar.gz	.txt	.tsv	.md5
PlusPF-8	PlusPF with DB capped at 8 GB	9/4/2024	5.5	7.5	.tar.gz	.txt	.tsv	.md5
PlusPF-16	PlusPF with DB capped at 16 GB	9/4/2024	11	15	.tar.gz	.txt	.tsv	.md5
PlusPFP	Standard plus Refeq protozoa, fungi & plant	9/4/2024	138	188	.tar.gz	.txt	.tsv	.md5
PlusPFP-8	PlusPFP with DB capped at 8 GB	9/4/2024	5.2	7.5	.tar.gz	.txt	.tsv	.md5
PlusPFP-16	PlusPFP with DB capped at 16 GB	9/4/2024	10	15	.tar.gz	.txt	.tsv	.md5
core_nt Database	Very large collection, inclusive of GenBank, RefSeq, TPA and PDB	9/4/2024	181.8	233.3	.tar.gz	.txt	.tsv	.md5
June, 2024
Viral	Refeq viral	6/5/2024	0.5	0.6	.tar.gz	.txt	.tsv	.md5
MinusB	Refeq archaea, viral, plasmid, human¹, UniVec_Core	6/5/2024	7.1	10.2	.tar.gz	.txt	.tsv	.md5
Standard	Refeq archaea, bacteria, viral, plasmid, human¹, UniVec_Core	6/5/2024	60	78	.tar.gz	.txt	.tsv	.md5
Standard-8	Standard with DB capped at 8 GB	6/5/2024	5.5	7.5	.tar.gz	.txt	.tsv	.md5
Standard-16	Standard with DB capped at 16 GB	6/5/2024	11	15	.tar.gz	.txt	.tsv	.md5
PlusPF	Standard plus Refeq protozoa & fungi	6/5/2024	64	83	.tar.gz	.txt	.tsv	.md5
PlusPF-8	PlusPF with DB capped at 8 GB	6/5/2024	5.5	7.5	.tar.gz	.txt	.tsv	.md5
PlusPF-16	PlusPF with DB capped at 16 GB	6/5/2024	11	15	.tar.gz	.txt	.tsv	.md5
PlusPFP	Standard plus Refeq protozoa, fungi & plant	6/5/2024	135	182	.tar.gz	.txt	.tsv	.md5
PlusPFP-8	PlusPFP with DB capped at 8 GB	6/5/2024	5.1	7.5	.tar.gz	.txt	.tsv	.md5
PlusPFP-16	PlusPFP with DB capped at 16 GB	6/5/2024	11	15	.tar.gz	.txt	.tsv	.md5
May, 2024
nt Database	Very large collection, inclusive of GenBank, RefSeq, TPA and PDB	5/30/2024	684	889	.tar.gz	.txt	.tsv	.md5
January, 2024
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
November, 2023
nt Database	Very large collection, inclusive of GenBank, RefSeq, TPA and PDB	11/29/2023	550	710	.tar.gz	.txt	.tsv
October, 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, 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, 2023
nt Database (ISSUE: see below)	Very large collection, inclusive of GenBank, RefSeq, TPA and PDB	5/2/2023	360	480	.tar.gz	.txt
March, 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, 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, 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, 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, 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, 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, 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

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.
The full PFP index releases, from June 2022–October 2023, as well as all the NT index releases were distributed with truncated Bracken database files. The truncated files were generally in the 10s or 100s of KB in size, significantly smaller than their non-truncated versions. Apologies for this error, which went unnoticed for a while. This was resolved as of the January 2024 release of PFP and will be resolved in the upcoming release of NT.

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.