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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 for metatranscriptomic comparison of viral abundance #138

Open smcnew opened 3 years ago

smcnew commented 3 years ago

Hi Jennifer:

I am trying to figure out if Bracken is appropriate for my analysis and haven't been able to find out for sure in the documentation or other forums.

I sequenced total mRNA from 40 samples and am trying to figure out if viral abundance varies among samples. I classified each sample separately using Kraken2, and found that the virus I'm looking for is present in the samples. However, now I would like a way to compare the number of reads among samples. I am able to generate relative abundance reports for each sample using Bracken, but I'm not sure how to approach comparing different samples.

Is there a way to do this with Bracken? Is Bracken appropriate to use with transcriptomic data? Thanks for any advice.

jenniferlu717 commented 3 years ago

I personally have not tested Bracken with transcriptomic data but I think that it can work for your purposes. We have a few downstream analysis scripts in KrakenTools: https://github.com/jenniferlu717/KrakenTools one of which may be what you are looking for. If you check in the DiversityTools section of KrakenTools, we have a script that can calculate alpha diversity.

We also have another script to be added soon that calculates beta diversity differences between samples,which I hope will be released within the next week.