Question

script to filter contigs >1kb

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9.2 years ago

krp0001 ▴ 40

Hi

I have been looking for a script that could filter out the contigs 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%)

genome Assembly • 5.5k views

ADD COMMENT • link updated 2.0 years ago by Ram 43k • written 9.2 years ago by krp0001 ▴ 40

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Another option, using the BBMap package:

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

It's very fast. Also supports maxlength.

ADD REPLY • link updated 2.0 years ago by Ram 43k • written 9.2 years ago by Brian Bushnell 20k

Ram · Answer 1 · 2015-02-05

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9.2 years ago

iraun 6.2k

Maybe this post can solve your issue.

ADD COMMENT • link updated 2.0 years ago by Ram 43k • written 9.2 years ago by iraun 6.2k

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Thanks !

That really helped. perfect!

ADD REPLY • link updated 4.5 years ago by Ram 43k • written 9.2 years ago by krp0001 ▴ 40

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You're welcome :)

ADD REPLY • link updated 2.0 years ago by Ram 43k • written 9.2 years ago by iraun 6.2k