Myself Nithya, currently working as a Bioinformatics Programmer at Scigenom labs, Cochin, Kerala,India.I am very new to the field of next generation sequencing. I have got some doubts regarding the output generated by SPAdes. Hope you can help me in this regard. The questions are as follows:
1. Did the assembly program combine the sequences into scaffolds using runs of N's to represent gaps between ordered and oriented contiguous sequences?
2. Does every N in the scaffold represents a gap? Alternatively, does the sequence include single or short runs of N's that represent ambiguous base calls?
Waiting forward for your reply.