New in v11
The fastx_syncpairs command sorts paired reads so that the reads appear in the same order in both files. If a read label appears in one file and not the other, it is discarded. The input files can be in FASTA or FASTQ format.
usearch -fastx_syncpairs fwd.fq -reverse rev.fq -output1 fwd_sorted.fq -output2 rev_sorted.fq