Required for nucleotide searches. Value must be set to plus or both.

-strand option

Staggered read pairs

If the paired read length is longer than the biological sequence in the construct, then the reads overflow into the sequencing primer and adapter sequences which bind the construct to the flow cell as shown below. I call this a "staggered" pair.

Staggered read pairs

The fastq_mergepairs command discards any "overhangs" at the ends of the reads which do not align to the other read.