GFA to Fasta file

Question

[marcela.uliano]

Hey guys,

Does anyone have a script (or a awk line) to extract fasta reads from a GFA file?

 

I've runned this miniasm in some Pacbio reads I have, and I would like to extract the final unitigs from the final file I have (which is a GFA file) in the fasta format!

 

Thanks a lot guys!

[marcela.uliano]

Awesome!!

Thank you so much!

[Atu]

Hi,

could you describe what does GFA stand for? I don't know about this format.

[ropolocan]

GFA is the Graphical Fragment Assembly format. Here is a post by Heng Li (@lh3) on this: https://lh3.github.io/2014/07/19/a-proposal-of-the-grapical-fragment-assembly-format.

Answer 1

[lh3]

awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa