Quality control of fastq read files
The first step of any analysis involving high-throughput sequencing data should consist of assessing the quality of the read data, possibly followed by the removal of low-quality reads.
It is possible to filter sequencing reads using Qiime, but a comprehensive report is not produced in the process. The FastQC program may be used to produce such a report, optionally followed by read filtering using the Trimmomatic program.
See here for an overview.