After denovo assembly, most algorithms (I am using Allpaths in this case) do scaffolding. This places contigs into scaffolds bridged by NNNNNN sequences.
I wanted to visually validate these bridges of NNNN sequences by mapping mate pairs back to the assemblies and checking the links. This is difficult to do because I have to manually search for these bridges.
Is there any tool, that provided a fasta file can annotate all "NNNNNN" regions into a bed file let's say? I am wondering if this can even be coded with perl simply.