Kraken protocols

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Kraken statistics

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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



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Publication for Kraken

Kraken in pipelines

PMCID: 5766104
PMID: 29329292
DOI: 10.1371/journal.pone.0189898

[…] 0.33 [] at the q20 level. reads containing ribosomal rna (rrna) sequences were erased from the dataset to avoid mis-annotation of rrnas as putative proteins [] using sortmerna version 2.0 []. the kraken taxonomic sequence classification system version 0.10.5 [] was applied to filter out prokaryotic sequences. those reads belong potentially to microorganisms co-inhabiting tree holes […]

PMCID: 5839586
PMID: 29509797
DOI: 10.1371/journal.pone.0193820

[…] and trimmed at both 5’ and 3’ ends using trimmomatic [] to filter out reads of low quality (phred quality score <30, length <36 bp). potential contaminating sequences were checked using kraken []; sequencing errors were corrected using lighter []. corrected reads were de novo assembled with spades 3.5.0 []; assembly quality was evaluated by quast []. contigs of >200 bp […]

PMCID: 5885014
PMID: 29498619
DOI: 10.1099/mgen.0.000162

[…] protocol and sequenced on an illumina hiseq2000 device with 100-cycle paired-end runs to give an average depth of 85-fold. taxonomic identity was assigned to all short reads and assemblies using kraken []. multilocus sequence types (sts) were derived from illumina read data using an in-house tool, available at de novo multi-contig draft […]

PMCID: 5896039
PMID: 29642940
DOI: 10.1186/s40168-018-0451-2

[…] 5 gb). trimmomatic v_0.36 was used to remove low quality sequences. human sequences were removed after alignment with reference genome (hg38 database []) using bowtie2 v_2.2.9, with default settings. kraken v_0.10.5-beta was then used to for taxonomic classification of unmapped microbial reads []. by the default setting of kraken, only complete genome sequences were included as the reference genom […]

PMCID: 5897366
PMID: 29651035
DOI: 10.1038/s41598-018-24280-8

[…] within the galaxy platform, with a galaxy web server instance supported by the national microbiology laboratory, public health agency of canada (phac nml galaxy). a custom workflow integrating kraken taxonomic classification tools and the amrplusplus resistome analysis pipeline tools was setup in galaxy to obtain simultaneous outputs for both resistome and microbiome analyses […]

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Kraken in publications

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] 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, […]

PMCID: 5920190
PMID: 29700147
DOI: 10.1128/genomeA.00299-18

[…] 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 […]

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

[…] 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) ()., samples were stored at −80°c prior to analysis. urine samples were subjected to vortex mixing and then centrifuged at 1,600 × g for 10 min […]

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

[…] databases maintained within a research group, into an analysis pipeline. additional plugins were implemented to support the most recent tools used for metagenome analysis, such as centrifuge, kraken, or ghostx. finally, the well-known mothur and qiime suites have recently been integrated into conveyor, extending the applicability of mgx from metagenomes to the analysis of 16s rrna […]

PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] have been developed to reduce this time by using alternatives to classical alignment. one approach is to match k-mers with a reference, as used in facs (stranneheim et al., ), lmat (ames et al., ), kraken (wood and salzberg, ), taxonomer (flygare et al., ), and metlab (norling et al., ). exact k-mer matching is generally faster than alignment, but requires a lot of computer memory. another […]

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Kraken review

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