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:file
Coordinates of each prophage identified in the genome, and their att sites (if found).
*.{tsv}
gbk
${prefix}.gb*:file
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
File containing the PhiSpy execution log
*.{log}
information
${prefix}_prophage_information.tsv:file
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:file
Genome with prophage regions masked with N.
*.{fasta}
bacteria_gbk
${prefix}_bacteria.gbk:file
Genome sequences identified as bacterial.
*.{gbk}
phage_fasta
${prefix}_phage.fasta:file
Phage sequences extracted from the genome.
phage_gbk
${prefix}_phage.gbk:file
prophage_gff
${prefix}_prophage.gff3:file
Prophage information in GFF3 format.
*.{gff3}
prophage_tbl
${prefix}_prophage.tbl:file
File containing prophage number and its location in the genome.
*.{tbl}
prophage_tsv
${prefix}_prophage.tsv:file
A file containing simpler version of the coordinates file, with only prophage number, contig, start and stop.
versions
versions.yml:file
File containing software versions
versions.yml
Prophage finder using multiple metrics
