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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

 (109)
call_split

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
call_split See protocol

[…] re 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 (). […]

call_split

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

2018
Front Microbiol
PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792
call_split See protocol

[…] ach 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 (; ). […]

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

[…] distribution of DNA base composition and synonymous codon usage of 33,256 archaeal amoA genes to identify possible molecular patterns associated with their global diversification (Fig. ; interactive Krona chart in Supplementary Data ). Additionally, we compared these properties in all protein-coding genes from 35 genomes of AOA (hereafter referred to as “genomic”) with those of their respective f […]

call_split

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
call_split See protocol

[…] 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 []. […]

call_split

Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH

2018
PMCID: 5884125
PMID: 29755805
DOI: 10.1155/2018/9230143
call_split See protocol

[…] those phyla which appeared in 75% of the samples were selected. The relative abundance of the genera present in all 10 soil samples was plotted by a heatmap and graphically represented by interactive Krona charts. β-Diversity or community similarity analysis was done by determining the pairwise distances using the phylogenetic distance metric, UniFrac generated by QIIME []. Monte Carlo simulations […]

library_books

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

[…] second largest functional group detected in both bioreactor fractions, accounting for 14 and 16% of the proteins identified in the grass biofilms and leachate samples (Figure and interactive view of Krona plots). Chaperones are essential for protein folding but also for the re-folding of stress-denatured proteins. Numerous GroEL (60 kDa) and GroES (10 kDa) chaperonins were detected and assigned, […]

Citations

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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.