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}

fasta (file)

Contigs/scaffolds identified as viral

*.{fna,fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bins (directory)

Directory containing bin FASTA files

**/vRhyme_best_bins_fasta/

membership (file)

TSV file describing the contig/scaffold membership of each bin

vRhyme_best_bins.*.membership.tsv

summary (file)

TSV file summarizing the attributes of each bin

vRhyme_best_bins.*.summary.tsv
author
Github user CarsonJM
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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).

github.com/AnantharamanLab/vRhyme 10.1093/nar/gkac341