I also find Megahit to be much faster and use far less memory compared to Spades, though Spades assemblies have moderately better continuity, when it finishes. But Spades is not currently suitable for metagenomes beyond very simple ones. Generally, resources permitting, I recommend running both Spades and Megahit and using the Spades assembly if it finishes, and otherwise the Megahit assembly. But if you have to pick just one, it's Megahit.

Vijay thanks alot for specifying one problem for me. can you please tell me that will there be one contig file after assembly by using r1 and r2 or multiple file i mean one for each ?

Thank you Brian. I was also thinking about using megahit if possible can you please provide a tutorial of megahit ? It will be a great favour to me.