Creating assembly graphs .gfa

Question

[ricardoguerreiro2121]

Hello all,

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.

Cheers,
Ricardo

[ramiroricardo]

I have the same question. It would be great to get some tips on how to do this.

Answer 1

[Asaf]

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.

[ricardoguerreiro2121]

What if I try to do an assembly using my scaffolds as reads. Wont it build an assembly graph for them?

Answer 2

[tothepoint]

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.