for one of the novel fungi, we did illumina mi-seq paired end sequencing and used velvet to assemble, I have 15500 contigs.
some information about reads (after removing adapters and poor quality bases):
Encoding : Sanger / Illumina 1.9
Total Sequences : 1747634
Sequence length : 36-301
If I had extra/additional reads I could have tried scaffolding or gap filling. Is there any option to reduce number of contigs?
Thanks Bhagya C T