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Question: GFA to Fasta file
3
gravatar for marcela.uliano
5.0 years ago by
marcela.uliano • 60
European Union
marcela.uliano • 60 wrote:

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!
sequence • 6.3k views
ADD COMMENT • link •
modified 5.0 years ago • written 5.0 years ago by marcela.uliano • 60
1

Awesome!!

Thank you so much!

ADD REPLY • link modified 18 months ago by h.mon ♦ 31k • written 5.0 years ago by marcela.uliano • 60

Hi,

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

ADD REPLY • link modified 11 months ago by _r_am ♦ 31k • written 5.0 years ago by Atu • 0

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.

ADD REPLY • link written 2.3 years ago by ropolocan • 680
10
gravatar for lh3
5.0 years ago by
lh3 ♦ 32k
United States
lh3 ♦ 32k wrote:
awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa
ADD COMMENT • link modified 11 months ago by _r_am ♦ 31k • written 5.0 years ago by lh3 ♦ 32k
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