Hi,

I have analysis with Qiime of 16s reads, and I want to make a pie chart with Krona but do not know which file from Qiime to use for Krona?


> Hi, hope this answer is not too late. :)

## convert biom to tsv format

    biom convert -i single_sample.biom -o single_sample.tsv --to-tsv --table-type "OTU table" --header-key taxonomy

## remove the first two rows with comment

    # take a look at single_sample.tsv
    $ head single_sample.tsv 
    # Constructed from biom file
    #OTU ID	H2O	taxonomy
    346085	140.0	Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas; Brevundimonas_bullata
    10298	2.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus; Photorhabdus_temperata
    122823	3.0	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Massilia; EF516371_s
    130468	2.0	Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingopyxis; Sphingopyxis_witflariensis
    139977	38.0	Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Erythrobacter; Erythrobacter_flavus
    121751	2.0	Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Catonella; JX096343_s
    96934	10.0	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas; Pseudomonas_guguanensis
    95181	4.0	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae; Acinetobacter; Acinetobacter_radioresistens

    # remove the comments
    $ egrep -v "^#" single_sample.tsv > sample_no_comment.tsv

## remove the first column

    $ cut sample_no_comment.tsv -f 2- > sample.tsv
    $ head -n2 sample.tsv 
    140.0	Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas; Brevundimonas_bullata
    2.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus; Photorhabdus_temperata

## replace the "; " with "\t"

    $ sed -i 's/;\s*/\t/g' sample.tsv
    $ head -n2 sample.tsv 
    140.0	Bacteria	Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Brevundimonas	Brevundimonas_bullata
    2.0	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales      Enterobacteriaceae	Photorhabdus	Photorhabdus_temperata

## now we can make a pie chart with ktImportText(One of the Krona tools)

    $ ktImportText -n enjoy_your_life -o sample.krona.html sample.tsv

## open sample.krona.html with your web browser, you'll see this
![Krona_snapshot_enjoy_your_life][1]

## all in one command(optional)

    $ awk -F '\t|;' 'BEGIN{OFS="\t"} FNR > 2 {$1=""; print $0}' single_sample.tsv | cut -f 2- > sample.tsv

  [1]: https://preview.ibb.co/hLhkoQ/Krona_snapshot_enjoy_your_life.png