Bracken specifications

Unique identifier:
OMICS_11751
Software type:
Package/Module
Restrictions to use:
None
Input format:
Tab-delimited columns
Output format:
Tab-delimited columns
Programming languages:
Perl, Python
Computer skills:
Advanced
Maintained:
Yes
Name:
Bayesian Reestimation of Abundance after Classification with KrakEN
Interface:
Command line interface
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)
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
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Stability:
Stable
  • Eubacteria
  • Viruses

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

Bracken distribution

download

Bracken support

Maintainer

  • Jennifer Lu <>

forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

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

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.

User review

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

Related Tools