I have paired end reads which I mapped to a reference genome. This genome contains two types of contigs. First are contigs with NC identifiers, which represent chromosomes and second type are contigs with NW(NW_XXXXXX) identifiers, which should be supercontigs with gaps.
The questions are: What are these NW contigs? Are they a part of NC contigs or independent units? What should I do when one end of paired end read aligns bouth to NW and NC contigs and another aligns only to NC?