Description

Binning virus genomes from metagenomes

Input

name:type
description
pattern

meta:map

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

]

reads:file

Preprocessed FASTQ file containing sample reads

*.{fastq}

meta:map

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

]

fasta:file

Contigs/scaffolds identified as viral

*.{fna,fasta,fa}

Output

name:type
description
pattern

bins

meta:map

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

]

vRhyme_best_bins_fasta/:directory

Directory containing bin FASTA files

**/vRhyme_best_bins_fasta/

membership

meta:map

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

]

**/vRhyme_best_bins.*.membership.tsv:file

TSV file describing the contig/scaffold membership of each bin

vRhyme_best_bins.*.membership.tsv

summary

meta:map

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

]

**/vRhyme_best_bins.*.summary.tsv:file

TSV file summarizing the attributes of each bin

vRhyme_best_bins.*.summary.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

vrhyme
GPL v3 GPL v3 license

vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).