Is it possible to create a .gfa file out of a fasta file?
This is outputted by some assembly programs and is great for assembly visualization in bandage. But I have now scaffolded my assembly and would like to visualize that as well.
These files are generated in the assembly process using software like e.g. flye.
Usually assemblers do the process of reads -> assembly graph -> assembly (contigs or scaffolds). The graphs are intermediates and represent repeats and branches, basically uncertainties in the assembly process. You can't go back from an assembly to a graph.
Yes, by SibeliaZ you can get .gfa file out of a fasta file. They recently updated there old version and now large genome file can also be used for the same.
I have the same question. It would be great to get some tips on how to do this.