I would pellet the phages on an ultra centrifuge with sucrose cushion 15% and do phenol chloroform extraction with the dried pellet. Then take your nucleotides pool and do deep sequencing. To discriminate DNA and RNA use RNAses or DNAses.

Dr . Juan Reguera  

thank you very much, your  answer will useful for me please if you have any articles about this protocol shar it to me 

karrar sir , how can you isolated the phages from sources and how can u confirm the phages ,  r u done plaque assay with respective bacteria, if done send me the protocol for plaque assay ,,,pleaseeeeee

hello Pallavali Rojarani 

this some articles that help me in isolated phage from marine water .

and i   use plaque method for isolate it in brief  i took sample water then i filtered it 0.22 then i mixed my bacteria  in mid log phase with   simple that was filtered for 15 m then i put mixed in warm top agar and pour it in plate contain solid agar after that i wait 72 h and look wether plaque form or not    

thank u mr. karrar, i isolated  and conformed the phages by using the above protocols successfully.