How to remove poor quality sequences from a fasta file?

Question

[Kumar]

I have a fasta file, which consist of thousands of viral genomes. I need to remove poor quality genomes which contain more than 30% NNNNNNN. Therefore, kindly help me to do the same.

[GenoMax]

I need to remove poor quality genomes which contain more than 30% NNNNNNN.

You can't assume that those genomes are poor quality. Perhaps that region is just not sequenced. N's are also used to pad/indicate areas that are not sequenced/sequenceable using current technologies.

[Kumar]

I agree @genomax, But these sequences are creating problems while alignment, that is why I would like to remove the same. I have good sum of viral genomes, therefore, I would like to keep precise base called genomes rather than the NNNN contains genomes.

Answer 1

[microfuge]

UCSC browser utils has a binary which does exactly that available here http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faFilterN

faFilterN - Get rid of sequences with too many N's

usage: faFilterN in.fa out.fa maxPercentN

[Kumar]

Thank you @microfuge. I have one clarification, in the command line maxPercentN should be replaced by 30 or 30%?

[microfuge]

From what I remember Just the number without percentage sign.

[GenoMax]

What do you think? Will % be a valid input for an option?

[Mensur Dlakic]

My rule of thumb: If doing something takes less than 10 seconds and can't hurt anyone, I just do it. Writing a question and waiting for a response is guaranteed to take longer than that.

[Kumar]

I regret for the same.