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Popular tool citations

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Protocols

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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Versioning


No version available

Documentation


Maintainer


  • person_outline Brian Ondov

Publication for Krona

Krona citations

 (74)
library_books

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

2018
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 […]

library_books

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

2018
Front Microbiol
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 […]

library_books

Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes

2018
Nat Commun
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 […]

library_books

Fungal community profiles in agricultural soils of a long term field trial under different tillage, fertilization and crop rotation conditions analyzed by high throughput ITS amplicon sequencing

2018
PLoS One
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) […]

call_split

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

2018
Front Microbiol
PMCID: 5871674
PMID: 29619022
DOI: 10.3389/fmicb.2018.00540
call_split See protocol

[…] (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 […]

library_books

Development and evaluation of a culture free microbiota profiling platform (MYcrobiota) for clinical diagnostics

2018
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.