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Question: Creating assembly graphs .gfa
1
gravatar for ricardoguerreiro2121
9 months ago by
ricardoguerreiro2121 • 60
Germany
ricardoguerreiro2121 • 60 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.

Cheers,
Ricardo
bandage graph gfa visualization assembly • 549 views
ADD COMMENT • link •
modified 8 months ago by Asaf ♦ 8.4k • written 9 months ago by ricardoguerreiro2121 • 60

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

ADD REPLY • link written 8 months ago by ramiroricardo • 0
2
gravatar for Asaf
8 months ago by
Asaf ♦ 8.4k
Israel
Asaf ♦ 8.4k 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 COMMENT • link written 8 months ago by Asaf ♦ 8.4k

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

ADD REPLY • link written 7 months ago by ricardoguerreiro2121 • 60
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