creating one abundance table of my samples using kraken2 output files
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12 months ago

I have obtained kraken outputs (2 files per sample) for my metagenomic sequencing data. Now, I want to create an abundance table with rows corresponding to the samples in my data and columns representing organisms found in my all samples. Is there any specific tool for doing that or should I use my own scripts to create such a table?

metagenomics visualization abundance kraken2 • 1.2k views
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without example files, and expected output, it is difficult to post a solution. For combining kraken reports, https://github.com/jenniferlu717/KrakenTools/blob/master/combine_kreports.py.

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I know this is not a specific answer to your question, but You could check out the R package Pavian (https://github.com/fbreitwieser/pavian)

Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn

It let you visualize and export abundance comparison tables and produces interactive sankey diagrams for each sample.