Question: script to filter contigs >1kb
0
gravatar for krp0001
5.0 years ago by
krp000120
Sweden
krp000120 wrote:

 

Hai, 

I have been looking for a script that could filter out the contaigs which are >1kb. my assembled file has the following stats. could some one help me with the script to get contigs >1kb. I have been through all the post for the similar script but couldn't find a right one. thanks in advance. 

Contig statistics:

Total length:    49295072 (n:27000)

Max:    788230

N20:    149300 (n:40)

N50:    57668 (n:200)

N80:    10314 (n:808)

n > 1kb:    2485

Tot bp in contigs > 1kb:    45136108 (91.563124%)

assembly genome • 2.6k views
ADD COMMENTlink written 5.0 years ago by krp000120

Another option, using the BBMap package:

reformat.sh in=contigs.fasta out=filtered.fasta minlength=1000

It's very fast. Also supports maxlength.

ADD REPLYlink modified 3 months ago by RamRS25k • written 5.0 years ago by Brian Bushnell17k
2
gravatar for iraun
5.0 years ago by
iraun3.7k
Norway
iraun3.7k wrote:

Maybe this post can solve your issue: How To Filter Multi Fasta By Length??.

ADD COMMENTlink written 5.0 years ago by iraun3.7k

Thanks !

That really helped. perfect!

ADD REPLYlink modified 3 months ago by RamRS25k • written 5.0 years ago by krp000120

You're welcome :)

ADD REPLYlink written 5.0 years ago by iraun3.7k
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