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