Quality control

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.