I have a whole genome sample from a phage/bacteria (little is known about the sample). I did the assembly with CLC genomics workbench and did a BLASTn for the scaffolds where I am getting hits from many organisms along with hits from a particular bacteriophage of interest (i know the phage speices but not the specific strain).
Now from the blast results, there are several hits for several strains of that phage. How can I be sure about the strain?
Strain level identification is a tough nut to crack unless you have reference genomes available for all strains. You may want to increase stringency of your BLAST (e.g. disallow gaps, mismatches) if you want to narrow down the list of possibilities.