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.
1 answer
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.
Log in to answer this question.
-
vg gbwt missing sample and haplotype metadata when created using minigraph-cactus with vg construct
written by cassiwatt •
-
Stable coordinates in gaf files?
written by Uveyik •
-
Distinguishing gfa and rgfa files
written by guntul •
-
How to generate a GAF that shows alignments to all component genomes in graph
written by peterdfields •
-
Vg Call error multiple paths detected using HPRC-GRCH38 ref
written by Alexandria A. •
-
Inject haplotypes into rGFA?
written by agd27 •
-
VG autoindex with pangenome constructed using minigraph-cactus
written by Marion •
