Description

Assess the quality of metagenome-assembled viral genomes.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

fasta file

*.{fasta,fna,fa}

db (directory)

Directory pointing to checkV database

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]

versions (file)

File containing software versions

versions.yml

quality_summary (file)

CheckV’s main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs

${prefix}/quality_summary.tsv

completeness (file)

CheckV’s detailed overview table on estimating completeness

${prefix}/completeness.tsv

contamination (file)

CheckV’s detailed overview table on estimating contamination

${prefix}/contamination.tsv

complete_genomes (file)

CheckV’s detailed overview table on the identified putative complete genomes

${prefix}/complete_genomes.tsv

proviruses (file)

CheckV’s extracted proviruses contigs

${prefix}/proviruses.fna

viruses (file)

CheckV’s extracted virus contigs

${prefix}/viruses.fna

Tools

checkv
BSD License

Assess the quality of metagenome-assembled viral genomes.