[Feature] Organize kraken2 minimizer data

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Problem

Hi taxprofiler group,

Thank you for building this practical tool!

I am using it to organize kraken2 results. I am looking for a method to organize kraken2 minimizer data. As you know, there are two optional columns in kraken2 results reporting total and distinct minimizers. Is there a way to organize these two columns into a table? Perhaps I can move them to the read count column and ask taxpasta to organize as if they are total counts?

Thanks,
Yuandong

Solution

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Alternatives

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Anything else?

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[Midnighter]

The original intent of taxpasta is quite minimal:

The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.

I agree that this information is useful downstream, but since we might aggregate across taxonomic ranks, I am hesitant to add a feature to bring arbitrary source columns into the final result simply because of the burden it puts on us to maintain that. I will think about it a bit more.