annotation for viral genome

[honey]

I am working on chipseq data for virus and wonder is there a tool to annotate the genome. I have FAStq file as well as NCBI accession no which will have all annottaions. Doing mannual may add errors and time consuming so I am trying to find if there is smart tool available out. Once I have chip tag enriched I can map the genome reggions back to their annottaion.


Thanks

[Torst]

Is the virus assembled into a contiguous sequence?

Is it an accession number for the sequence, or the short reads?

[honey]

annotation for viral genome

It has NCBI accession number.

[Torst]

It has NCBI accession number.

What is the accession number?