Hi, everyone! I have a question that how to call a consensus sequence that could fill gaps located in the reference. Whether samtools could do this? We know that PacBio long reads could use to scaffold the contigs. However, it left the gaps with NNNNN. As the PacBio long reads do not have NNNN on it. Why do they use NNNN to replace the original seuqence?

The case is like this:

contig: contig1 contig2 contig3

                     AAAAAAAAAA             TTTTTTTTTTT                CCCCCCCCCCCC

Subreads:

                  GGGAAAAAAAAAAGGGGGGGGGGGGGTTTTTTTTTTTGGGGGGGGGGGGGGGGCCCCCCCCCCCCGGG

Scaffold:

                     AAAAAAAAAANNNNNNNNNNNNNTTTTTTTTTTTNNNNNNNNNNNNNNNNCCCCCCCCCCCC

So, I am wonder by using samtool or other tools, is there can call a consensus sequence is like this:

Consensus:

                  GGGAAAAAAAAAAGGGGGGGGGGGGGGTTTTTTTTTTTGGGGGGGGGGGGGGGCCCCCCCCCCCCGGG

how to call this consensus? Thanks!