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jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
http://ccb.jhu.edu/software/bracken/index.shtml
GNU General Public License v3.0
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compatibility for downstream processing using other metagenomic tools #12

Open ajaybabu27 opened 7 years ago

ajaybabu27 commented 7 years ago

Hi,

I am looking to do further downstream analysis of the bracken data using Qiime. Do you guys happen to have a conversion script that can output a biom format table from the bracken output ?

Also it would be nice to have a krona compatible output too.

Thanks, Ajay.

jenniferlu717 commented 7 years ago

I currently do not have either conversion script but I could look into it and see what I can do in the next couple of days.

ajaybabu27 commented 7 years ago

Thanks ! I actually found a third party tool that uses the kraken report format to build a biom file: https://github.com/smdabdoub/kraken-biom

I am currently testing it out using the report file output from bracken. Looks good so far. Let me know if you see any inconsistencies in the above mentioned tool.

Ajay.

sungenomics commented 7 years ago

Hi @jenniferlu717,

Is there a way to generate Krona plots with Bracken results ?

Thanks, Thibaut

RojasBorja commented 6 years ago

Hi, I have bracken reports and I do not know how to plot them. Does anyone knows? Has anyone resolved this before? I am also looking a way to plot them on phyloseq or something similar. I have been investigating but got no results.

Thank you for your attention,

Borja

jenniferlu717 commented 5 years ago

I would just load it into excel and just make a bar plot of it all. It really depends on the number of genomes/taxons in your output. Do you care only about the top species and is there a cutoff for the ones you care about?