Quality control of fastq read files

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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.