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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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##Bracken metagenomics abundance #26

Closed penglbio closed 6 years ago

penglbio commented 6 years ago

I am little confused by counting the abundance of species in metagenomics-wide sequencing. If we used the read counts as the abundance of the species, shall we normalize it. Liking the RNA-seq, maybe need to divide the length, because the length of the each microbial genome is different. So I want to ask if the result of Bracken report can be used to compared diversity of the species abundance directly.

jenniferlu717 commented 6 years ago

If you do want to use the output of the Bracken report to estimate the number of organisms and not just number of reads, you will need to normalize by average genome length for the species. Bracken only provides the estimated read counts originating from a species, not the estimate organism numbers.

penglbio commented 6 years ago

but In your paper, according to my understanding, The figure 5,you just use the read counts to estimate of species abundance. I think the bacteria genome length of each specie is different. so just using read counts may be not correct completely