Bracken specifications


Unique identifier OMICS_11751
Name Bracken
Alternative name Bayesian Reestimation of Abundance after Classification with KrakEN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Percentage of reads for the subtree rooted at this taxon, Total number of reads for the subtree rooted at this taxon, Number of reads assigned directly to this taxon level, Taxonomical Rank [U, -, D, P, C, O, F, G, S], NCBI Taxonomy ID, Scientific Name - Indented (2 spaces per level)
Input format Tab-delimited columns
Output data Name, Taxonomy ID, Level ID (S=Species, G=Genus, O=Order, F=Family, P=Phylum, K=Kingdom), Kraken Assigned Reads, Added Reads with Abundance Reestimation, Total Reads after Abundance Reestimation, Fraction of Total Reads
Output format Tab-delimited columns
Operating system Unix/Linux
Programming languages Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • Eubacteria
  • Viruses



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  • person_outline Jennifer Lu <>

Bracken article

Bracken institution(s)
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Applied Physics Laboratory, Johns Hopkins University, Baltimore, MD, USA; Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
Bracken funding source(s)
This work was supported in part by the U.S. National Institutes of Health under grants R01-HG006677 and R01-GM083873, and by the U.S. Army Research Office under grant W911NF-1410490.

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