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USEARCH v11
 New in v11 

fastx_syncpairs command

 
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.

Example

usearch -fastx_syncpairs fwd.fq -reverse rev.fq -output1 fwd_sorted.fq -output2 rev_sorted.fq