remove zero abundance OTUs after filtering samples

[ConstantinoSchillebeeckx]

I tend to work with very large OTU tables that contain results from multiple studies. Often times, my first step in my workflow is to whittle the OTU table down to just the samples I'm interested in using filter_samples_from_OTU_table.py - in some cases, this leaves OTUs in my table that have no abundance across any of the remaining samples.

It might be nice to have a flag to remove those OTUs from the table in the same sample filtering step instead of having to call filter_otus_from_otu_table.py with the -n 1 option.

[jairideout]

👍 Note that we aren't adding new features to QIIME 1 (except for fixing critical bugs). QIIME 2 will automatically remove empty samples or features when using qiime feature-table filter-features and qiime feature-table filter-samples, respectively. QIIME 2 is alpha software but you might consider trying it out.