Hi Aiden Lab! I was taking a look at the recently published Myotis lucifugus HiC-enhanced assembly (https://www.dnazoo.org/assemblies/Myotis_lucifugus) and got to wondering what determined the N's in the newest assembly. If I recall correctly, the initial Broad assembly work was done using older sequencing techniques where insert libraries had relatively fixed lengths, thus the gaps (N's) in a scaffold could be known with relatively high precision. Because multiple, distinct inserts were used by Broad, the different lengths of N's reflected the different insert sizes. This would be different from some of the more modern assembly tools that simply insert a constant value of N's regardless of the distance between contigs. Is there somewhere in your documentation where the number of N's inserted are described? The newest assembly has different numbers of N's as well, but I wasn't sure whether these distances were known, as in the Broad assembly, or basically unknown.
Thanks very much!