Biowulf High Performance Computing at the NIH
KronaTools

      


A set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files

Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. KronaTools can be used to create Krona charts from several bioinformatics tools and raw data formats. The resulting interactive charts are self-contained and can be viewed with any modern web browser.

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Reference

Creating Krona Graphs
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KronaTools can be used to generate Krona charts using data from many different sources. See the Krona GitHub Wiki for ideas. One of the simplest example uses for KronaTools is to generate a Krona chart detailing disk usage. (User input in bold.)

[user@biowulf ~]$ sinteractive --mem=40g --cpus-per-task=4
salloc.exe: Pending job allocation 36461269
salloc.exe: job 36461269 queued and waiting for resources
salloc.exe: job 36461269 has been allocated resources
salloc.exe: Granted job allocation 36461269
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0123 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn0123 ~]$ module load kronatools
[+] Loading kronatools 2.7 on cn0123

[user@cn0123 ~]$ ktImportDiskUsage -o test.html /usr/local/apps/samtools

You can view the resulting Krona chart here.

Although this is useful, Krona was designed to visualize metagenomic data. In the following example, we will generate a Krona chart based on a simulated dataset processed using CLARK. First, we'll allocate an interactive session and copy some test data to our data directory.

[user@cn0123 ~]$ module load clark
[+] Loading clark 1.2.3
[user@cn0123 ~]$ cd /data/$USER
[user@cn0123 user]$ mkdir -p dbd2/Custom
[user@cn0123 user]$ cp $CLARK_TEST_DATA/complex_targets/*.fna dbd2/Custom
[user@cn0123 user]$ cp $CLARK_TEST_DATA/complex_reads.fa .

Now we'll build a custom bacteria database, run a classification on it, and estimate abundance.

[user@cn0123 user]$ set_targets.sh dbd2 bacteria --species
[...snip...]
[user@cn0123 user]$ classify_metagenome.sh -O complex_reads.fa -R complex \
             -n $SLURM_CPUS_PER_TASK
[...snip...]
[user@cn0123] estimate_abundance.sh -F complex.csv -D dbd2 --krona
[...snip...]

Finally, we'll use ktImportTaxonomy from the KronaTools suite to generate a Krona chart in .html.

[user@cn0123 user]$ module load kronatools
[+] Loading kronatools 2.7 on cn0123

[user@cn0123 user]$ ktImportTaxonomy -i -m 3 -o krona_taxonomy.html results.krn

You can view the resulting Krona chart here.

Documentation
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