Description

Run NCBI’s FCS adaptor on assembled genomes

Input

Name (Type)
Description
Pattern

meta (map)

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

]

assembly (file)

assembly fasta file

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

cleaned_assembly (file)

Cleaned assembly in fasta format

*.{cleaned_sequences.fa.gz}

adaptor_report (file)

Report of identified adaptors

*.{fcs_adaptor_report.txt}

log (file)

Log file

*.{fcs_adaptor.log}

pipeline_args (file)

Run arguments

*.{pipeline_args.yaml}

skipped_trims (file)

Skipped trim information

*.{skipped_trims.jsonl}
maintainers
Github user d4straub
Github user gallvp
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Tools

fcs
United States Government Work

The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly.

ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools github.com/ncbi/fcs/wiki/FCS-adaptor https://github.com/ncbi/fcs