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Merging 2 x 250 reads with long overlap

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_pctid 80:

usearch -fastq_mergepairs *R1*.fastq -relabel @ -fastq_maxdiffs 10 -fastq_pctid 80 \
  -fastqout merged.fq