mask contigs in scaffolds by length

[Wallysb01]

Hello,

I have been doing some de novo assembly, and have a set of scaffolds that I am fairly happy with. However, I would like to mask some short contigs in these scaffolds.

I had retained short contigs (<200bp) if they were scaffolded together, then I attempted gap filling, but still some short contigs remain and fall below some thresholds for submitting data or different types of downstream analysis.

So, I'd really just rather turn them into Ns, which would allow me to keep the other, more contiguous parts of the scaffolds.

Does anyone know of a tool that would do this? I haven't come up with much in my searches.

Thanks