Rank in rGFA files

Question

[tsnorri]

The rGFA format requires that each segment record has a rank which is specified with the SR tag. If the segment is on a linear reference genome, the rank should be zero, and otherwise a positive number.

It is unclear to me how the ranks should be assigned. For example, should each stable sequence (as specified with the SN tag) have a distinct rank, or is such an approach sufficient to provide input for e.g. Minigraph?

I checked Google and The design and construction of reference pangenome graphs with minigraph but so far could not find an answer.

Answer 1

[colindaven]

I watched this nice up to date video from Glenn Hickey, one of minigraph-cactus authors. It mentions how minigraph, which uses rGFA format, builds up pangenomes sequentially and should answer your question.

[tsnorri]

Thanks! I’ll check it on Monday.