I assembled paired-end genome sequences using SOAPdenovo, and got some scaffold sequences.
I found GapCloser program which is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, and ran it against my scaffold sequences.
However I found the GapCloser trimmed 'N' in scaffold sequences only. Should do I remove 'N' sequence in scaffold? Is it mandatory step?
Thanks for your comment in advance.