Gapclosing metagenomic islands v1

This protocol allows gapclosing of metagenomic islands which occur when mapping metagenomic reads to a phage reference genome. These gaps arise because multiple gene variants co-exist for specific points on the genome, these variants fluctuate in dominance over space and time. This means mapping metagenomic reads from one location onto a phage reference genome from another will often result in multiple metagenomic islands. These gaps can be closed with the following protocol, allowing the other gene variants present in a phage pan-genome to be detected. The protocol relies on detection of the same phages in similar ecosystems and relies on the phage being sequenced to sufficient depth in each sample to allow metagenomic assembly of large contigs (>10 X coverage). Prerequisites: Bowtie2 Geneious software package SPAdes assembler Blast+ tools