Simple script to generate Krona charts for all samples in an OTU table file
This bash script needs the KronaTools to be installed and also a tab delimited file with OTU numbers and taxonomy.
Clone this repository in you linux machine, make it executable and you are ready to go.
git clone https://github.com/GenomicaMicrob/OTUsamples2krona.git
cd OTUsamples2krona
chmod +x OTUsamples2krona.v0.2.3.shIf you do not have git installed, just download the zip file, unzipped it and proceed as above.
./OTUsamples2krona.v0.2.3.sh samples-tax.tsv
The test file samples-tax.tsv is also included. This file was created with mg_classifier from samples from P. Schloss Miseq SOP webpage.
For help:
./OTUsamples2krona.sh -h
The OTU file has to have the following format: The first line has the sample name (delimited by tabs) and a taxa structure (although this structure is not strictly necessary), from the second line downwards, the OTU values (delimited by tabs) and the taxonomy delimited by semicolons.
A B C domain;phylum;class;order;family;genus;species
48 10 0 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Photobacterium;Unclassified_s
10 0 14 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Vibrio;Unclassified_s
0 0 3 Bacteria;Actinobacteria;Actinobacteria_c;Micrococcales;Microbacteriaceae;Limnoluna;Limnoluna_rubra
93 278 777 Bacteria;Cyanobacteria;Chroobacteria;Chroococcales;Prochlorococcaceae;Prochlorococcus;AM084273_s
9 0 66 Bacteria;Cyanobacteria;Chroobacteria;Chroococcales;Prochlorococcaceae;Prochlorococcus;BX548175_s
...From this example file (samples-tax.tsv, included), the script will create three html files in a subdirectory named krona. The sample name will appear at the center of the pie chart generated.
If you use QIIME, during the standard pipelines, the file otu_table.biom is produced, this file can be converted to the format needed with biom (of course you have to have biom installed):
biom convert -i otu_table.biom -o otu_table.tsv --to-tsv --header-key taxonomy
This command will produce a file almost ready to use; since a column at the beggining is added with no useful data, we need to delete it with:
cut -f1 --complement otu_table.tsv > otu.tsv
Sometimes the taxonomy structure produced by QIIME is rather crappy, due to the crappy databases it uses, so it might not work all the time. Consider using mg_classifier, a super fast classifier that produces the file samples-tax.tsv with the correct format.