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The orientation or direction of a sequence is its directionality with respect to a reference sequence. There are always two possible orientations -- forward and reverse. The reverse complement of a sequence is that same sequence with flipped orientation. The forward and reverse-complement forms of a sequence may be represented as F/R, or as fw/rc, or as +/-.

Orientation is most often discussed in the context of input reads. The input fasta files give no indication of a read's orientation. Instead, each read's entry in the XML ancillary files contains a tag, trace_end, that specifies its orientation. If an insert gives rise to a read pair, the two reads will have opposite orientations.

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