Hello,
I am seeing a discrepancy between Sequence Tube Map visualization and what the same sequences look like when inspected outside STM.
I built a circular vg graph reference (all reference paths are closed/circular). I embedded a named ORF path in the graph, then mapped either metagenomic assembled contigs or raw reads to the graph using vg (GAM output).
In Sequence Tube Map, alignments frequently appear as many spirals/loops (often ~8–10 apparent loops) but, when I inspect the same sequences with BLAST , they look mostly colinear. I also do not see evidence of strong tandem repeats that would justify so many loops: at most I would expect ~1–2 repeat-driven loops in the reference or the query.
Importantly, I observe the same spiral/loop pattern also when mapping raw reads, so this does not seem to be an assembly artifact.
Could Sequence Tube Map display many apparent loops on circular references due to visualization/layout choices or graph representation, even if the underlying GAM alignment is not repeatedly traversing the same nodes? What is the best way to confirm whether the GAM alignment truly revisits the same nodes (non-simple path) versus being a simple traversal that only looks spiral in Sequence Tube Map?
I can share a minimal example (small GFA/XG + one GAM + screenshots) and provide versions/commands if needed.
Thank you very much for developing and maintaining this tool, it has been extremely helpful for visualization graph alignments.
Hello,
I am seeing a discrepancy between Sequence Tube Map visualization and what the same sequences look like when inspected outside STM.
I built a circular vg graph reference (all reference paths are closed/circular). I embedded a named ORF path in the graph, then mapped either metagenomic assembled contigs or raw reads to the graph using vg (GAM output).
In Sequence Tube Map, alignments frequently appear as many spirals/loops (often ~8–10 apparent loops) but, when I inspect the same sequences with BLAST , they look mostly colinear. I also do not see evidence of strong tandem repeats that would justify so many loops: at most I would expect ~1–2 repeat-driven loops in the reference or the query.
Importantly, I observe the same spiral/loop pattern also when mapping raw reads, so this does not seem to be an assembly artifact.
Could Sequence Tube Map display many apparent loops on circular references due to visualization/layout choices or graph representation, even if the underlying GAM alignment is not repeatedly traversing the same nodes? What is the best way to confirm whether the GAM alignment truly revisits the same nodes (non-simple path) versus being a simple traversal that only looks spiral in Sequence Tube Map?
I can share a minimal example (small GFA/XG + one GAM + screenshots) and provide versions/commands if needed.
Thank you very much for developing and maintaining this tool, it has been extremely helpful for visualization graph alignments.