As with any other NGS experiment, metagenome data should be quality controlled before any downstream analysis. The filtering steps may include adapter removal, quality trimming, and filtering out low-quality reads. Moreover, depending on the sample type and preparation procedures, metagenomic reads may contain host DNA, which should be removed. Other QIIME 2 plugins already provide generalized functionality to address quality filtering/control of next-generation sequencing data — the MOSHPIT plugin suite expands on these by focusing more on host DNA removal from metagenome data. The next sections contain a brief overview of the filtering steps which can be done using QIIME 2 and MOSHPIT.