Fig. 1

The reference flow workflow: Reads are aligned to reference genome in the first pass. Reads with high mapping quality alignments are “committed.” Unaligned reads or reads with low mapping quality are “deferred” and re-aligned to one or more additional references. The process can iterate, with similar logic for how reads are committed or deferred to another pass. Deferrals could follow the shape of an overall “reference flow graph.” Once all alignments are complete, alignments are merged. For a read aligning to more than one reference, only the best is reported, with ties broken arbitrarily. Alignments are translated (“lifted over”) to the coordinates of a standard reference like GRCh38