See also
fastq_mergepairs command
fastq_mergepairs options
With very long overlaps such as typical 2 x 250 V4 you will sometimes find that it is better to allow more differences in the alignment; see example report. For example, you might choose to increase set -fastq_maxdiffs 10 -fastq_maxdiffpct 10:
usearch -fastq_mergepairs *R1*.fastq -sample @ -fastq_maxdiffs 10 -fastq_maxdiffpct
10 \
-fastqout merged.fq