Predict prophages in bacterial genomes
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
Genome file in .gbk or .gbff format.
Coordinates of each prophage identified in the genome,
and their att sites (if found).
A duplicate GenBank record that is the same as the input record,
but we have inserted the prophage information, including att
sites into the record.
File containing the PhiSpy execution log
File containing all the genes of the genome, one per line.
The tenth column describes how likely the gene is a phage gene.
Genome with prophage regions masked with N.
Genome sequences identified as bacterial.
Phage sequences extracted from the genome.
Prophage information in GFF3 format.
File containing prophage number and its location in the genome.
A file containing simpler version of the coordinates file,
with only prophage number, contig, start and stop.
File containing software versions
Prophage finder using multiple metrics