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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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Taxa abundance and species diversity from Kraken and Bracken reports #107

Open marcjermaine-pontiveros opened 4 years ago

marcjermaine-pontiveros commented 4 years ago

Hi!

I'm trying to determine the taxa abundance of Kraken assigned reads. Currently, I'm using the CladeReads from Pavian package in R to compute the phylum-level composition but I'm not sure if this is a correct approach. I'm planning to extract the assigned reads from the reports directly and use vegan package in R to determine abundance and their relation across the samples, and species diversity. Thank you very much!

jenniferlu717 commented 4 years ago

Kraken itself does not abundances. At the phylum level, you might be getting most of the reads but maybe not all if any read is stranded at the root or kingdom levels. Bracken is designed for abundances and just gives a table with all of the read abundances.

We don't have scripts yet available for comparison across samples but some are in development now.