I made de novo transcriptome assembly using about 300 millions PE reads (100bp from Illumina) with different k-mers. Several assembled transcriptome was merged and exposed to CAP3. Then, I used SSPACE-standard tool (version 3) to generate scaffold using the command of "perl SSPACE_Standard_v3.0.pl -l libraries.txt -s file1.fasta -k 5 -a 0.7 -m 50 -x 1 -T 3 -b output1". However, it sounds that scaffolding did not significantly improve the assembly. Actually, the number of initial contigs and scaffold were about 87000 and 85000, respectively. Similarly, N50 was 960 bp and 980 bp before and after scaffolding, respectively. It will be great if you share me any opinion or experience about it. How to improve more scaffolding step?