Setting filtering thresholds after taxonomic assignment


When we do the taxonomic assignment what cut-off was used for absence/presence of a taxon in each group e.g. in what proportion of the group did the taxon need to be present to be considered present in the group?

Thank you


Hello again @annsantos,
I have adjusted the title of this topic to better describe your question (to make it more searchable by others with the same issue!)

The taxonomy classifiers do not take abundance into account when classifying… they classify whatever sequences are given as input.

This is something that would be done up/downstream in your workflow, and is largely based on your own workflow decisions. Singletons/rare features are filtered by default by the denoising methods, depending on which method you used. You can also use the filter-features method to filter features based on abundance or prevalence thresholds.

So to clarify: these proportions are defined by you in separate actions. This is done so by design, to give you better control over the process.


May be i put the question wrong. What i want to know is that determines if an ASV is e.g streptococcus. OTUs are sequences clusters that differ by less than a dissimilarity threshold, normally 3%, that is, those OTUs sequences represent a certain taxonomic unit with 97% similarity. And ASV?

Hi @annsantos,
I recommend checking out the overview tutorial and the literature cited in there to get a better idea of the differences between these steps. It sounds like you are conflated a few distinct processes: denoising, abundance filtering (which is often included in the denoising pipelines as I mentioned above), and taxonomy classification.

taxonomy classification. These do not take abundance into account.

ASVs are unique sequence variants… see the overview tutorial and especially the original publications on those methods for a better description of what they do. You can think of ASVs as 100% OTUs that have had some quality filtering applied to remove/correct sequencing errors.

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