Velvet assembler and scaffold

[Rahul shelke]

hello,
My contigs.fa file generated from velvet assembly contains NNNNNNN base in every sequences.
so does it mean that my contigs.fa file is scaffold file or only assembly file?
If not can I generate good scaffolds by using velvet.....?

used command....
for velvetg
velvetg out_data_29 -clean yes -exp_cov 21 -cov_cutoff
2.81 -min_contig_lgth 200


Thanks

[paa6]

in my opinion NNNNNNN shows gaps. may be u need to check quality of ur reads before going for assembly. try FastQC.