Predict prophages in bacterial genomes
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
gbk
:file
Genome file in .gbk or .gbff format.
*.{gbk,gbff}
coordinates
${prefix}.tsv
Coordinates of each prophage identified in the genome, and their att sites (if found).
*.{tsv}
${prefix}.gb*
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.
log
${prefix}.log
File containing the PhiSpy execution log
*.{log}
information
${prefix}_prophage_information.tsv
File containing all the genes of the genome, one per line. The tenth column describes how likely the gene is a phage gene.
bacteria_fasta
${prefix}_bacteria.fasta
Genome with prophage regions masked with N.
*.{fasta}
bacteria_gbk
${prefix}_bacteria.gbk
Genome sequences identified as bacterial.
*.{gbk}
phage_fasta
${prefix}_phage.fasta
Phage sequences extracted from the genome.
phage_gbk
${prefix}_phage.gbk
prophage_gff
${prefix}_prophage.gff3
Prophage information in GFF3 format.
*.{gff3}
prophage_tbl
${prefix}_prophage.tbl
File containing prophage number and its location in the genome.
*.{tbl}
prophage_tsv
${prefix}_prophage.tsv
A file containing simpler version of the coordinates file, with only prophage number, contig, start and stop.
versions
versions.yml
File containing software versions
Prophage finder using multiple metrics
