Krona protocols

View Krona computational protocol

Krona statistics

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Krona specifications

Information


Unique identifier OMICS_01498
Name Krona
Alternative names KronaTools, radiant
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Javascript, Perl, Shell (Bash)
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 2.7
Stability Stable
Source code URL https://codeload.github.com/marbl/Krona/tar.gz/v2.7
Maintained Yes
Wikipedia https://github.com/marbl/Krona/wiki

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Maintainer


  • person_outline Brian Ondov <>

Publication for Krona

Krona in pipelines

 (13)
2018
PMCID: 5796750
PMID: 29422788
DOI: 10.5423/PPJ.NT.08.2017.0190

[…] assembled using idba-ud ver. 1.1.1. () and contigs were aligned to the ncbi nucleotide database using blastn with an e-value cutoff of 1e-10. alignment results were classified taxonomically using krona tools (). bacteriophage contigs were extracted using an unshared program that we had developed. gene models were predicted using genemark.hmm with heuristic models ()., sequence analysis showed […]

2018
PMCID: 5871674
PMID: 29619022
DOI: 10.3389/fmicb.2018.00540

[…] (ec) numbers corresponding to the identified proteins are retrieved when available, minpath () is used to construct parsimonious pathways and ipath2.0 () is employed for pathway visualization. krona plots were constructed using the krona template () and circos plots using the circos online tool developed by ., non-metric multidimensional scaling (nmds) based on bray–curtis distances […]

2017
PMCID: 5264480
PMID: 28118849
DOI: 10.1186/s40168-016-0224-8

[…] pairs with matches identified by bwa to m. tuberculosis complex were searched against the nt database. figures representing the bacterial proportions in cancer and normal samples were created using krona []., the log10 ratio comparing the number of mycobacterium spp. read pairs per run to the total number of reads per run was calculated as the log10 of the number of mycobacterium spp. read […]

2017
PMCID: 5352169
PMID: 28117801
DOI: 10.3791/54936

[…] following the overlapping of reads using flash of reads, the resulting extended fragments underwent bacterial taxonomic classification using kraken software 7 and were subsequently visualized with krona software (figure 3)., the majority of the bacterial species present in the silage metagenome are found within 4 prokaryotic phyla: firmicutes (34%), actinobacteria (28%), proteobacteria (27%) […]

2017
PMCID: 5397476
PMID: 28473817
DOI: 10.3389/fmicb.2017.00685

[…] using a miseq sequencer (illumina; san diego, ca, usa)., to identify potential pathogens and detect antimicrobial resistance genes, sequencing reads were analyzed by the mepic2 (takeuchi et al., ), krona (ondov et al., ), and megan6 software (huson et al., , ). to identify the bacterial sequence type and antimicrobial resistance, sequencing reads were analyzed by multilocus sequence typing […]


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Krona in publications

 (68)
PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18

[…] of the archaeal community was aligned and annotated with the refseq database as a reference (). the taxonomic structure was then exported via the mg-rast api server () and further visualized using krona tool version 2.7 ()., list and composition of all 12 metagenomes uploaded and processed at the mg-rast server. metagenome sequences were obtained from total-community dna from bog vegetation […]

PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792

[…] filter fraction, and the sample as a whole, were defined as otus in 100% of samples determined with qiime’s compute_core_microbiome.py script (). core otus were then visualized using ggplot2, and krona (; )., the paired-end reads were quality trimmed using trimmomatic (ver. 0.36) (), merged with flash (ver. 1.2.11) (), and assembled de novo with metaspades (ver. 3.10.1) without read error […]

PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] a., figtree v1.4.3, http://beast.bio.ed.ac.uk/figtree, 2016), and environmental and molecular composition data were displayed in the phylogeny with itol v3, and in hierarchical charts using krona. mafft, muscle, probcons and probalign analyses were performed through the cipres science gateway, and emboss tools were used through the galaxy platform (http://usegalaxy.org)., custom python […]

PMCID: 5886558
PMID: 29621291
DOI: 10.1371/journal.pone.0195345

[…] fungal genera raw data were transformed into ranks to achieve normalized distribution for three-way-anova (shapiro-wilk, p = 0.05; brown-forsythe, p = 0.05) with post-hoc test holm-sidak (p = 0.05). krona plots (– files) to zoom into taxonomic assignments of treatment replicates were designed by using the interactive metagenomic visualization web browser []., in long-term average (2005–2014) […]

PMCID: 5948305
PMID: 29549470
DOI: 10.1007/s10096-018-3220-z

[…] of necs. all results are presented to the user as a single, interactive web report in galaxy using the ireport tool []. the ireport was designed to visualize the resultant microbiota profiles using krona [], list quantitative microbiota profiles in otu tables (with the microbial load per otu reported as 16s rrna gene copies), summarize results of diversity calculators, and provide an extensive […]


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Krona institution(s)
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA

Krona review

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senaj

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Desktop
Can be used with multiple metagenomic analysis tools like MEGAN, Kraken, and CLARK. Generates very appealing taxonomic graphics.