Phage DNA Extraction, Genome Assembly, and Genome Closure

Bacteriophages, or more simply phages, are currently experiencing a renaissance in life science research for their roles in natural microbial communities, their potential use as antimicrobials, and biotechnological applications. In the modern era, one of the primary steps in phage characterization is obtaining the sequence of the complete genome; this information can be used to determine the relationship of the phage to known phages, predict phage lifestyle, and is a prerequisite for many downstream applications. This protocol describes methods for determining the complete sequence of a double-stranded DNA bacteriophage genome, including DNA extraction from a phage lysate, sending the DNA out to a sequencing service, assembly of the sequence raw reads, and completion of the genome sequence.