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USEARCH v11

Read preparation: orient to same strand

See also
  OTU / denoising pipeline
  Read preparation
  Quality control: stand duplicates
 
Sometimes, reads have sequences on both strands. See strand duplicates for how to check. If you have reads on both strands, then use the orient command with the largest available database.

Example

usearch -orient reads.fq -db silva.udb -fastqout oriented.fq -tabbedout orient.txt