assembly_decontamination

Description¶

MGnify Production assembly decontamination subworkflow. Performs sequential decontamination of assembled contigs against the human genome, PhiX and a genome specified by the user (usually the sample host). It designed to remove any contigs that come from any of those references.

Installation¶

ebi-metagenomics/assembly_decontamination

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install assembly_decontamination

Pipelines¶

This subworkflow is used by the following pipelines:

assembly-analysis-pipeline

Components¶

This subworkflow uses the following components:

decontaminate_contigs (subworkflow)

Input¶

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information and decontamination parameters. Expected keys: - phix_reference: Filename prefix of PhiX reference genome (optional, null to skip) - human_reference: Filename prefix of human reference genome (optional, null to skip) - contaminant_reference: Filename prefix of custom contaminant reference (optional, null to skip)	-
`assembly`	file	Assembly FASTA file containing contigs to be decontaminated	`*.{fasta,fa,fna}`

Output¶

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information	-
`cleaned_contigs`	file	Decontaminated assembly FASTA file	`*.{fasta,fa,fna}`
`versions`	file	File containing software versions	`versions.yml`