Question

Creating assembly graphs .gfa

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4.9 years ago

ricardoguerreiro2121 ▴ 80

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

assembly gfa graph bandage visualization • 6.7k views

ADD COMMENT • link updated 10 months ago by Adam Taranto ▴ 40 • written 4.9 years ago by ricardoguerreiro2121 ▴ 80

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

ADD REPLY • link 4.8 years ago by ramiroricardo • 0

score 2 · Answer 1 · 2020-02-18

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4.8 years ago

Asaf 10k

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 4.8 years ago by Asaf 10k

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

ADD REPLY • link 4.7 years ago by ricardoguerreiro2121 ▴ 80

score 0 · Answer 2 · 2020-11-06

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4.1 years ago

tothepoint ▴ 940

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.

ADD COMMENT • link 4.1 years ago by tothepoint ▴ 940

score 0 · Answer 3 · 2024-01-18

You might want to convert a FASTA file to GFA format to edit it in a GFA-viz tool like Bandage.

You can use fa2gfa from GraphTagger to generate a basic gfa with segment length tags. You can add additional tags such as depth "DP" using csv2tag.

This graph won't have any links between contigs like you might see in a GFA output by an assembler. If you have long-reads available you can update the basic gfa with links using tools such as ntLINK or SGTK (skip scaffolding steps to just update the links if you want to manually curate the graph before scaffolding). You can also manually add link lines to a GFA using the format from the GFA-Spec.