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I did run kraken2 and I get two kinds of output How do I generate OTU table from these outputs for phyloseq usage?

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    $\begingroup$ Hi @twinkle if you don't get a response, maybe expand your question to provide details of your outputs? There are kraken users on the site. $\endgroup$
    – M__ ♦
    Commented Nov 12, 2020 at 22:34

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You need to run Bracken to the Kraken2 report output to estimate abundance.

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    $\begingroup$ I have multiple text file as output, and text file contains data like 2 column format with thousands of rows. from these type of outputs how do I generate OTU table $\endgroup$
    – twinkle
    Commented Nov 15, 2020 at 14:24
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    $\begingroup$ you will use the --report option output from Kraken2 like the input of Bracken for an abundance quantification of your samples. E.g. kraken2 --db ${KRAKEN_DB} --report ${SAMPLE}.kreport ${SAMPLE}.fq > ${SAMPLE}.kraken where ${SAMPLE}.kreport will be your input for Bracken. $\endgroup$
    – zorbax
    Commented Nov 16, 2020 at 11:43

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