OTU-table-to-KRONA-pie

This bash script is used to generate a one page KRONA pie html file from a rarified multi samples OTU table.

Prerequisites ⚡

• KronaTools have to be installed.
• The OTU table generated by QIIME renown 'otu_table.tsv' has to have the following format :

# Constructed from biom file
#OTU ID A	B	C	D	E	F	taxonomy
denovo7708	2.0	0.0	0.0	0.0	0.0	0.0	Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae; Legionella; uncultured bacterium
denovo3059	0.0	3.0	1.0	0.0	0.0	0.0	Bacteria; Bacteroidetes; Cytophagia; Cytophagales; Cytophagaceae; uncultured; uncultured bacterium
denovo3058	0.0	13.0	0.0	15.0	30.0	0.0	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales
denovo3051	1.0	2.0	0.0	0.0	2.0	3.0	Bacteria; Proteobacteria; Gammaproteobacteria; X35; uncultured bacterium
denovo3050	2.0	20.0	1.0	19.0	27.0	0.0	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae
...

You can also specify the path to your table as a parameter. sh OTUtable2KRONA.sh myfile/amazing_otu_table.tsv