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