In the SOP we refer both to QIIME and QIIME2. QIIME2 is more of a platform / command line interface than the original QIIME that contained a set of Python wrapper scripts. The QIIME developers suggest migrating to QIIME2.
vsearch is an open source alternative to usearch and our testing showed that it performs equally well on the H3ABioNet test dataset. There is no 64 bit memory limitation when using vsearch.
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