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marbl / Krona

Interactively explore metagenomes and more from a web browser.
https://github.com/marbl/Krona/wiki
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Is it possible to visualize a Qiime 1.9 OTU biom file #36

Open wjacobus opened 7 years ago

wjacobus commented 7 years ago

I've used qiime to generate an OTU table for my datasets. Is it possible to viz with Krona

ondovb commented 7 years ago

BIOM format is not officially supported, but it seems like you could use ktImportText after converting to TSV (I have not tried this): http://biom-format.org/documentation/biom_conversion.html

ondovb commented 7 years ago

It would be good to support BIOM officially.

darnassiano commented 7 years ago

Nope, I've converted it to tsv with biom, but had no results after :(

biom convert -i taxa_summary/filtered_otu_cc_greengenes_L7.biom --table-type="OTU table" --to-tsv -o L7.txt

darnassiano commented 7 years ago

Although, biom converted table can be visualized after adapting the data in the Excel Template.

GenomicaMicrob commented 7 years ago

Hi, I have created a little script to get all krona charts from an OTU table, check it here https://github.com/GenomicaMicrob/OTUsamples2krona Browse to the end of the README file, there is solution that might help.