Commands > Search, Reads
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.
The -tabbedout option is a tabbed text file giving the orientation of each
input sequence. Fields are: query_label, strand, plus_count, minus_count.
Strand is + or -.
Multithreading is supported.
usearch -orient reads.fastq -db 16s.udb -fastqout reads_plus.fq