orient command
Orient nucleotide sequences in a FASTA or FASTQ file to the same strand as a database.
The -fastaout option is a FASTA filename for the oriented sequences.
The -fastqout option is a FASTQ filename for the oriented sequences (requires FASTQ input).
The -notmatched option is an output file for sequences with undetermined orientation. It will be FASTA or FASTQ, depending on the input file format.
Multithreading is supported.
Example
usearch -orient reads.fastq -db 16s.udb -fastqout reads_plus.fq