How to cross-reference scaffolds/contigs with files in .gfa and .fastg?

[jolespin]

I'm trying to figure out how to cross-reference the identifiers in the assembly_graph_with_scaffolds.gfa, the assembly_graph.fastg, and scaffolds.fasta files.

[asl]

Hello

Scaffolds are represented as paths in the assembly graph. There are already P records in GFA for this (note that each record correspond to the scaffold segment as GFA does not allow gapped paths).

The same information is available standalone in scaffolds.paths file. Consider familiarising yourself with SPAdes manual (https://cab.spbu.ru/files/release3.15.4/manual.html#spadesoutput) for more information & examples