Question: Creating assembly graphs .gfa
gravatar for ricardoguerreiro2121
9 months ago by
ricardoguerreiro212160 wrote:

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.


ADD COMMENTlink modified 8 months ago by Asaf8.4k • written 9 months ago by ricardoguerreiro212160

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

ADD REPLYlink written 8 months ago by ramiroricardo0
gravatar for Asaf
8 months ago by
Asaf8.4k wrote:

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.

ADD COMMENTlink written 8 months ago by Asaf8.4k

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

ADD REPLYlink written 7 months ago by ricardoguerreiro212160
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