I use SOAPdenovo2 to assemble a large genome (4.8G) using ~20X paired-end reads. The  total length of contig sizes is 6.3G while total length of scaffolds is 2.7G. Note that this is a haploid genome, so there is no issue of heterozygosity for scaffolding. I am wondering what happened during the scaffolding procedure? How comes that sum of scaffolds is so much smaller than sum of contigs?
What causes the difference in total length of assembled contigs and scaffolds in SOAPdenovo2?
assembly;scaffold