Masking short sequences between gaps in genome assembly

Question

[pbigbig]

Hi,

I have assembled a genome, using Illumina Pair-end reads for assembling, Mate pair reads for scaffolding. In resulted fasta files, I notice some patterns like this:

...NNNNNNNNNNNNNNNNGTGTGTAGGATCTCACNNNNNNNNNNNNNNNNNNNNNN...

I would like to hardmask those small "island" sequences between gaps with defined maximum length (e.g masking if < 200bp), could you please give some suggestion?

Thank you very much in advance!

[Titus]

When you say masking do you mean remove it ?

[pbigbig]

Hi, I mean to hard masking it, which would turn any A C G T to N