Krona protocols

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description
Krona computational protocol

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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Documentation


Maintainer


  • person_outline Brian Ondov <>

Publication for Krona

Krona IN pipelines

 (6)
2018
PMCID: 5863371
PMID: 29562928
DOI: 10.1186/s40168-018-0432-5

[…] a high comparable percentage of maximum potential bitscore (within 10%) were retained for each contig as (alternative) secondary annotation. custom scripting (in python, r, shell, javascript) and krona [47] were used to generate images and figures (additional file 2)., to find coding regions within bacterial polycistronic sequences, we used transdecoder software […]

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

[…] the identified proteins are retrieved when available, minpath (ye and doak, 2009) is used to construct parsimonious pathways and ipath2.0 (yamada et al., 2011) is employed for pathway visualization. krona plots were constructed using the krona template (ondov et al., 2011) and circos plots using the circos online tool developed by krzywinski et al. (2009)., non-metric multidimensional scaling […]

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 [35]., 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: 5527411
PMID: 28490492
DOI: 10.1128/JCM.00462-17

[…] with kraken using different filtration thresholds. a threshold value of 0.15 provided optimum read classification sensitivity while minimizing spurious results. kraken output was visualized using krona (38)., the performance of metagenomic sequencing was assessed by comparing the species identified from sequencing data with the species isolated from sonication fluid samples considered culture […]

2015
PMCID: 4426941
PMID: 25983555
DOI: 10.4137/BBI.S12462

[…] offers a wide range of visualization tools for metagenomic annotation results. it supports multiple visualization schemes including functional or taxonomic dendrograms, tag clouds, bar charts, and krona taxonomic plots,113 that allow hierarchical data to be explored in the form of a zoomable pie chart., it is widely accepted that sequencing of the 16s rrna gene reflects eubacterial […]

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.