Home Software Services About Contact usearch manual
orient command
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