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USEARCH v11

Merging 2 x 300 reads with short overlap

See also
  fastq_mergepairs command
  fastq_mergepairs options

Default options for fastq_mergepairs typically work well for this case. Sometimes the R2 quality is bad; see Strategies for dealing with low-quality reverse reads (R2s). Example command-line:

usearch -fastq_mergepairs *R1*.fastq -sample @ -fastqout merged.fq