Description

A bacteriophage lifestyle prediction tool

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta:file

FASTA file containing phage contigs/scaffolds/chromosomes (if it is a multi-FASTA file be sure to add the --multi_fasta argument)

*.{fasta,fna,fa}

Output

name:type
description
pattern

bacphlip_results

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bacphlip:file

TSV file containing Temperate and Virulent scores for each phage sequence

*.bacphlip

hmmsearch_results

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.hmmsearch.tsv:file

TSV file containing binary output indicating gene presence/absence based on hmmsearch results

*.hmmsearch.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bacphlip
MIT

A Random Forest classifier to predict bacteriophage lifestyle