Kraken statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Kraken

Tool usage distribution map

This map represents all the scientific publications referring to Kraken per scientific context
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Associated diseases

This word cloud represents Kraken usage per disease context

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Kraken specifications


Unique identifier OMICS_04481
Name Kraken
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

Publication for Kraken

Kraken citations


American Gut: an Open Platform for Citizen Science Microbiome Research

PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] e were dropped. The characterization of the metabolites from the supernatant using HPLC-MS is discussed under “HPLC-MS analysis” above.Following assembly of the draft genomes, taxonomic assessment by Kraken () revealed that of the 119 successfully sequenced colony isolate cultures, 95 matched the bloom organisms identified by Amir et al. (). Compellingly, 70 of these isolate genomes contained exac […]


Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044
call_split See protocol

[…] 300 bp were then excluded from the final assembly. The statistical results of the assembly were estimated using QUAST (version 3.2) [].To examine sequencing reads for potential contamination, we used Kraken (version 1.0) [] with the standard Kraken database to check the paired-end DNA libraries. Classified reads reported by Kraken were further examined using our proposed pipeline (). Briefly, we e […]


Isolation of Oropouche Virus from Febrile Patient, Ecuador

PMCID: 5938787
PMID: 29664378
DOI: 10.3201/eid2405.171569

[…] –40 borderline, >40 negative) and negative results for the other pathogens. As an initial screen for other pathogens, we applied unbiased metagenomic sequencing. Analysis of sequencing reads by using Kraken, a system for assigning taxonomic labels to individual reads (), identified 1% reads (5,016 of 464,444) as specific to OROV. We generated an OROV consensus sequence by mapping reads to a refere […]


Draft Genome Sequence of Plant Growth Promoting Burkholderia sp. Strain BE12, Isolated from the Rhizosphere of Maize

Genome Announc
PMCID: 5920190
PMID: 29700147
DOI: 10.1128/genomeA.00299-18
call_split See protocol

[…] uenced at MicrobesNG ( using Illumina MiSeq and HiSeq 2500 technology platforms, with 2 to 250-bp paired-end reads. The closest existing reference genome was determined using Kraken (), and the reads were mapped using the Burrows-Wheeler Aligner (BWA) MEM algorithm ( to assess data quality. The reads were assembled by de novo assembly using S […]


A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

PMCID: 5915698
PMID: 29719871
DOI: 10.1128/mSystems.00044-18
call_split See protocol

[…] ic pathways produced by HUMAnN2 were derived from the MetaCyc database () and were the basis for analyses performed on microbial metabolic profiling. Taxonomic profiling was facilitated by use of the Kraken taxonomy assignment software tool (V.0.10.6) (). […]


Flexible metagenome analysis using the MGX framework

PMCID: 5937802
PMID: 29690922
DOI: 10.1186/s40168-018-0460-1

[…] axonomic classification workflow and compared its results to those of several established standalone tools, which were selected based on recency and reported frequency of use according to literature: Kraken [], Kaiju [], Centrifuge [], and MetaPhlAn 2 []. All tools were run with their respective default settings, with databases generated in May 2017, and classification performance was assessed at […]

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Kraken review

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Anonymous user #4386

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Easy and very powerful tool even if outputs are highly polluted by false positive results.