Creating assembly graphs .gfa
2
1
Entering edit mode
20 months ago

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 • 2.0k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
19 months ago
Asaf 8.6k

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
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
10 months ago
tothepoint ▴ 600

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

Login before adding your answer.

Traffic: 1470 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6