See also
fastq_mergepairs command
Introduction to paired read merging
The fastq_mergepairs command supports quality filtering by expected errors. The maximum number of expected errors is specified by the fastq_merge_maxee option, e.g.:
usearch -fastq_mergepairs SampleA_R1.fastq -fastqout merged.fq -fastq_merge_maxee 1.0
The number of expected error is a floating-point number. Using 1.0 specifies that the merged read should have zero as the most probable number of errors according to its Q scores.
Not recommended for making an OTU table
If you are going to create an OTU table, you should perform quality filtering as a separate step using the fastq_filter command. This is because many reads with >1 expected errors will map successfully to an OTU so you will get better sensitivity by mapping all reads.
Therefore, the best strategy is to perform OTU clustering or denoising (error-correction) with quality-filtered reads then create the OTU table (otutab command) using all merged reads before quality filtering.