Question: GFA to Fasta file
2
gravatar for marcela.uliano
3.6 years ago by
European Union
marcela.uliano50 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 • 3.9k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by marcela.uliano50
1

Awesome!!

Thank you so much!

ADD REPLYlink modified 6 weeks ago by h.mon26k • written 3.6 years ago by marcela.uliano50

Hi,

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

ADD REPLYlink written 3.6 years ago by Atu0

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 REPLYlink written 11 months ago by ropolocan560
7
gravatar for lh3
3.6 years ago by
lh331k
United States
lh331k wrote:
awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa
ADD COMMENTlink written 3.6 years ago by lh331k
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