Proportions on stacked barplot not summing up to 100

[ScaonE]

Dear all,

I ran OPAL and it yielded nice results in the Metrics tab.

One thing that worries me in the Gold standard tab, is that some stacked barplots do not sum to 100, see this pic:

I use a custom script to convert "typical" abundance tables (taxa as rows & samples as columns) to the Bioboxes profiling output format. Maybe something went wrong there?

Two questions:

• How can we explain the stacked barplots not summing up to 100?
• Is there some existing script for the conversion to Bioboxes profiling output format?

[fernandomeyer]

Thanks for the questions.

• The plots reproduce the contents of the gold standard, so it is likely that the abundances in your gold standard do not sum to 100% at the different taxonomic ranks. OPAL does not automatically normalize the abundances to 100% (since version 1.0.9), but you can still do so with option --normalize.
• We do not provide scripts for format conversion, as most profilers use their own format and we cannot support them all. Still, it is possible to copy and adapt scripts used by some bioboxes, for example, from https://github.com/CAMI-challenge/docker_profiling_tools.