Homeland Security Open Sources Software to Power Humanitarian Projects

Software originally developed at the at the U. S. Department of Homeland Security’s National Biodefense Analysis and Countermeasures Center (NBACC) to sequence DNA for biodefense is now being used by Microsoft to sequence mosquito DNA in the fight against disease.

Developed by the NBACC’s National Bioforensic Analysis Center Genomics Team for bioforensics applications, Krona is a unique visualization tool that enables users to quickly analyze massive quantities of data – such as more than 100 million sequences of DNA in a single mosquito sample, according to Microsoft. Mosquitoes collect blood samples from every animal and human they bite and in turn can be an early warning indicator of disease. Microsoft is using Krona to analyze the complex DNA collected by mosquitos.

The Krona software constructs a multi-layered, interactive chart that shows the relative abundance and diversity of prokaryotic and eukaryotic components in the sample. NBFAC scientists use Krona to visualize metagenomic datasets, which are often made up of millions or billions of individual DNA sequences that collectively tell the scientists what organisms are present in the sample being analyzed.  Metagenomic analysis is extraordinarily powerful, and is being used around the world to characterize what kinds of microbes are present in different environments.  The challenge is that metagenomics analyses generate a huge amount of data. The Krona tool provides a new way of viewing these huge datasets at different levels of complexity.  NBACC uses Krona to visualize and report metagenomic data from a wide range of metagenomic analyses, ranging from bioforensic analyses in support of federal law enforcement to collaborative work with NASA characterizing samples collected from the International Space Station.

Widely used around the world, Krona was released as an open-source software implemented in HTML5 and JavaScript, creating fully interactive charts that can be explored in a Web browser. Its interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages.

Krona has been embedded as the primary visualization tool in many different bioinformatics pipelines, including those developed by Harvard University, Imperial College of London, Erasmus Medical Center, and the University of Queensland.  It is also part of the standard metagenomic analysis pipelines provided by Illumina and Thermo Fisher for their sequencing instrument customers.

Krona is one of several bioinformatics tools developed by NBACC for bioforensic analysis that have been published, made available through open-source licenses, and used in a wide range of applications.

The Krona was first reviewed in a 2011 Bioinformatics journal article and was freely released to the scientific community under an open-source license. The Krona tool has been used in at least 250 scientific papers published in the scientific literature over the last five years.

The software is available at http://krona.sourceforge.net.