How NanoOK works

How NanoOK deals with alignments

If running with multiple reference sequences, a single query sequence may produce 1 or more alignments to 1 or more references. NanoOK adopts the following approach to assign reads to references:

1. Sort alignments in order of score. The read belongs to the reference with highest score.
2. Then merge any other alignments that align to the same reference as the highest scoring alignment, in order of score.
3. Any sections of these subsequent alignments that overlap with already merged alignments are discarded.

Where the highest score is shared by two or more identically scoring alignments, NanoOK choses one of them at random. This can result in very slight changes in alignment figures reported. If you wish deterministic behaviour, specify the -deterministic parameter.