Description

Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies

Input

name
description
pattern

meta

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

assembly

assembly fasta file

*.{fasta,fa}

Output

name
description
pattern

meta

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

versions

File containing software versions

versions.yml

fcsadaptor_cleaned_assembly

Cleaned assembly in fasta format

*.{cleaned_sequences.fa.gz}

fcsadaptor_report

Report of identified adaptors

*.{fcs_adaptor_report.txt}

fcsadaptor_log

Log file

*.{fcs_adaptor.log}

fcsadaptor_pipeline_args

Run arguments

*.{pipeline_args.yaml}

fcsadaptor_skipped_trims

Skipped trim information

*.{skipped_trims.jsonl}

fcs_gx_report

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)

*.fcs_gx_report.txt

fcsgx_taxonomy_report

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt