Description

Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

taxid{:bash}

:string

Taxonomy ID of the expected organism

fasta{:bash}

:file

Input genome assembly file in FASTA format

*.{fa,fasta,fna}

gxdb{:bash}

:directory

Directory containing the FCS-GX database

ramdisk_path{:bash}

:string

Path to RAM disk for improved performance (optional)

Output

name:type
description
pattern

fcsgx_report{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.fcs_gx_report.txt{:bash}

:file

Final contamination report with contaminant cleaning actions. Interpreted by gx clean genome to separate cleaned sequences from contaminants.

taxonomy_report{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.taxonomy.rpt{:bash}

:file

Intermediate report with assigned taxonomies to individual sequences.

*.taxonomy.rpt

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.summary.txt{:bash}

:file

FCSGX log file

*.summary.txt

hits{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.hits.tsv.gz{:bash}

:file

Save intermediate alignments

*.hits.tsv.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

fcsgx
NCBI-PD

The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.

github.com/ncbi/fcs-gx github.com/ncbi/fcs/wiki https://github.com/ncbi/fcs-gx 10.1186/s13059-024-03198-7
included in
genomeqc
maintainers
Github user tillenglert
Github user mahesh-panchal
get in touch
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